Cryptic polypeptides and uses thereof

ABSTRACT

The disclosure features, among other things, polypeptides comprising a Cryptic polypeptide, a functional fragment thereof, or variants of any of the foregoing. Also featured are nucleic acids encoding the polypeptides, methods for producing of the polypeptides, and a variety of diagnostic and therapeutic applications in which the polypeptides are useful. For example, the polypeptides can be used to treat a subject having a condition associated with bone loss.

RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No.62/109,376 filed Jan. 29, 2015, which is herein incorporated byreference in its entirety.

BACKGROUND

Bone loss is a serious clinical problem that is most commonly diagnosedin post-menopausal woman, but that can occur in all populations at allages. Marx (2004) Science 305:1420-1422 and Lotinun et al. (2012) CurrMol Pharmacol 5:195-204. Diseases, such as cancer, diabetes,inflammatory bowel disease, as well as inflammatory diseases requiringsteroid treatments, can suppress bone formation and lead to increasedfracture risk. Fractures associated with bone loss are a leading causeof hospitalization, disability, and premature mortality in the elderly,affecting over 2 million Americans and leading to 500,000hospitalizations and placing of 180,000 individuals into nursing homesevery year. Dempster (2011) Am J Manag Care 17(Suppl 6):5164-5169 andDawson-Hughes et al. (2012) Osteoporos Int 23:811-820. U.S. medicalcosts associated with osteoporotic fractures were nearly $17 billion in2005 and are estimated to accumulate to over $474 billion in 20 years.Blume and Curtis (2011) Osteoporo Int 22:1835-1844. Beyond increasingfracture risk, the skeleton serves a broad array of physiologicfunctions, and thus bone loss may directly affect glucose and insulinmetabolism, organ and vascular repair, as well as immune systemfunction. Ferron et al. (2010) Cell 142:296-308; Clemens and Karsenty(2011) J Bone Miner Res 26:677-680; Cappariello et al. (2014) ArchBiochem Biophys 558:70-78; and Charles and Nakamura (2014) CurrOsteoporos Rep 12:1-8.

Because of the magnitude of the problem, biotechnology andpharmaceutical companies have searched for therapeutics that slow, stop,or reverse bone loss. Regrettably, only one class of approved agentsrestores bone mass, and all approved agents have important limitationsand side effects that impact their efficacy and long-termadministration. Thus, there remains an urgent need for noveltherapeutics that are well tolerated and effectively stimulate boneformation to restore bone mass.

SUMMARY

The disclosure is based, at least in part, on the discovery that Crypticprotein can bind to Activin A and Activin B and inhibit the ability ofActivins A and B not only to bind to their cognate cellular receptor(s),but also to signal through those receptor(s). Inhibition of Activin Ahas been shown to promote bone formation in vivo, and, thus, Cryptic andpolypeptides comprising Cryptic (or variants and functional fragmentsthereof) are useful in a variety of therapeutic applications forincreasing bone formation, bone mass, bone density, bone strength, andthe like. For example, the polypeptides described herein are useful fortreating subjects suffering from a condition associated with bone loss,such as osteoporosis or Paget's disease. Moreover, the inventors havedetermined that while Cryptic binds with high affinity to Activin A,Cryptic binds with lower affinity to the transforming growth factor betasuperfamily proteins GDF-11 or myostatin (GDF-8) (Table 1). Inhibitionof myostatin signaling in vivo has been shown to promote muscle mass,whereas inhibition of GDF-11 promotes erythropoiesis. Thus, while thedisclosure is not bound by any particular theory or mechanism of action,the Cryptic polypeptides described herein are useful for treating bonedisorders and have a reduced secondary effect (or no secondary effect)on muscle growth and/or erythropoiesis as compared to other Activin Ainhibitors, such as soluble Activin RIIA and Activin RIIB molecules.

Accordingly, in one aspect, the disclosure features a polypeptidecomprising a Cryptic protein, a functional fragment thereof, or avariant thereof. In some embodiments, the Cryptic protein is a mammalianprotein (or the functional fragment or variant is derived from themammalian Cryptic protein). In some embodiments, the Cryptic protein isa human protein (or the functional fragment or variant is derived fromthe human Cryptic protein). In another aspect, the disclosure features apolypeptide comprising: (i) the amino acid sequence depicted in any oneof SEQ ID NOs:1 to 9, 19, or 20; (ii) a variant of the amino acidsequence depicted in any one of SEQ ID NOs: 1 to 9, 19, or 20 having notmore than 40 (e.g., not more than 39, 38, 37, 36, 35, 34, 33, 32, 31,30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13,12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1) amino acid substitutions,deletions, insertions, or a combination of any of the foregoing; or(iii) an amino acid sequence that is at least 70 (e.g., at least 75, 80,85, 90, 95, or 99) % identical to any one of the amino acid sequencesdepicted in SEQ ID NOs: 1 to 9, 19, or 20.

In some embodiments, the polypeptide comprises the amino acid sequencedepicted in SEQ ID NO:7, 8, or 9. In some embodiments, the polypeptidecomprises an amino acid sequence that is at least 95% identical to anyone of the amino acid sequences depicted in SEQ ID NOs: 1 to 9, 19 or20. In some embodiments, the polypeptide comprises, or consists of, theamino acid sequence depicted in SEQ ID NO:10. In some embodiments, thepolypeptide comprises the amino acid sequence depicted in SEQ ID NO: 19or 20.

In some embodiments, the polypeptide comprises an amino acid sequencethat comprises any one of SEQ ID NOs: 4-9, wherein the amino acidsequence is at least 70 (e.g., at least 75, 80, 85, 90, 95, or 99) %identical to the amino acid sequence depicted in SEQ ID NO: 1 or 2.

In some embodiments, the polypeptide binds to human Activin A with aK_(D) of less than 1×10⁻⁹M, less than 1×10⁻¹⁰ M, less than 1×10⁻¹¹M, orless than 1×10⁻¹²M. In some embodiments, the polypeptide binds to humanActivin A with a K_(D) of between about 200 picomolar to about 1picomolar (e.g., between about 200 picomolar and about 100 picomolar,between about 100 picomolar and about 50 picomolar, between about 50picomolar and about 1 picomolar, between about 150 picomolar and 1 aboutpicomolar). In some embodiments, the polypeptide binds to human ActivinA with a K_(D) of between about 500 picomolar and about 50 picomolar.

In some embodiments, the polypeptide has at least 5 (e.g., at least 10,15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or99) % of the ability of wild-type human Cryptic to inhibit human ActivinA-dependent cell signaling in vitro. In some embodiments, thepolypeptide has a higher affinity for human Activin A or inhibitsActivin A to a higher degree than does wild-type human Cryptic (e.g.,assayed as part of a fusion protein with IgG1 Fc).

In some embodiments, the polypeptide binds to human Activin B with aK_(D) of less than 1×10⁻⁹M or less than, or equal to, 5×10⁻¹⁰ M. In someembodiments, the polypeptide binds to human Activin B with a K_(D) ofbetween about 500 picomolar to about 1 nanomolar (e.g., between about300 picomolar to about 1 nanomolar, about 200 picomolar to about 700picomolar, or about 250 picomolar to about 800 picomolar).

In some embodiments, the polypeptide has at least 5 (e.g., at least 10,15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or99) % of the ability of wild-type human Cryptic to inhibit human ActivinB-dependent cell signaling in vitro. In some embodiments, thepolypeptide has a higher affinity for human Activin B or inhibitsActivin B to a higher degree than does wild-type human Cryptic (e.g.,assayed as part of a fusion protein with IgG1 Fc).

In some embodiments, the polypeptide comprises a heterologous moietythat increases the serum half-life of the polypeptide in a subject. Theheterologous moiety can, in some embodiments, comprise all or part of analbumin protein. In some embodiments, the heterologous moiety comprisesan immunoglobulin Fc constant region (e.g., SEQ ID NO:17 or 21). Forexample, in some embodiments, the polypeptide comprises the amino acidsequence depicted in SEQ ID NO:1, 2, 19, or 20, and the amino acidsequence of an Fc constant region (e.g., SEQ ID NO: 17 or 21). In someembodiments, the polypeptide comprises the amino acid sequence depictedin any one of SEQ ID NOs:4 to 9, and the amino acid sequence of an Fcconstant region.

In some embodiments, a linker (e.g., one or more amino acids) canseparate the Cryptic, variant, or functional fragment thereof from theheterologous moiety. In some embodiments, the linker can have the aminoacid sequence depicted in SEQ ID NO:18. In some embodiments, asdescribed below, the linker can contain a protease cleavage site, suchas the cleavage site for TEV protease.

In some embodiments, the polypeptide does not include a linker sequence.

In some embodiments, the polypeptide is a fusion protein. In someembodiments, the fusion protein comprises the amino acid sequencedepicted in SEQ ID NO:10.

In some embodiments, the heterologous moiety comprises polyethyleneglycol (PEG).

In some embodiments, the polypeptide comprises a heterologous moietythat targets the polypeptide to bone. The heterologous moiety thattargets the polypeptide to bone can comprise, e.g., the formula: X_(n),wherein X is a canonical or noncanonical amino acid that has a negativecharge at physiological pH and n is an integer from 1 to 40. X can be,e.g., aspartic acid or glutamic acid. n can be an integer between 1 and30, e.g., 10 and 16, 2 and 20, 1 and 20, 5 and 20, 3 and 20, 5 and 15,10 and 15, 10 and 20, 10 and 30, 10 and 25, or 10 and 30. In someembodiments, n is at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15.In some embodiments, n is less than 25, 24, 23, 22, 21, 20, 19, 18, 17,16, 15, 14, 13, 12, 11, or 10.

In some embodiments, the heterologous moiety is a detectable label.

In some embodiments, the polypeptide can be a monomer. In someembodiments, the polypeptide can, in the presence of a second copy ofthe polypeptide, form a dimer or multimer. For example, in embodimentsin which the polypeptide is a fusion protein comprising all or part of aCryptic polypeptide fused to an IgG Fc region, the polypeptide candimerize by way of the Fc region. In some embodiments, the polypeptidecomprises a dimerization or multimerization domain, e.g., an Fc regionor any other polypeptide (or functional portion thereof) capable ofdimerizing.

In another aspect, the disclosure features a pharmaceutical compositioncomprising any one or more of the polypeptides described herein and apharmaceutically-acceptable carrier, excipient, or diluent.

In another aspect, the disclosure features a pre-filled syringecomprising one or more of the polypeptides described herein.

In another aspect, the disclosure features a kit comprising apharmaceutical unit dosage form of one or more of the polypeptidesdescribed herein, a means for administering the one or more polypeptidesto a subject, and, optionally, instructions for administration, e.g.,self-administration.

In another aspect, the disclosure features a nucleic acid comprising anucleotide sequence encoding any one of the polypeptides describedherein. Also featured is a vector, e.g., an expression vector,comprising the nucleic acid.

In another aspect, the disclosure features a host cell comprising thevector or expression vector. The host cell can be eukaryotic (e.g.,yeast, insect, mammalian, or plant) or prokaryotic. In some embodiments,the host cell is a rodent cell (CHO cell) or a non-human primate cell(COS cell). In some embodiments, the host cell is an NSO cell.

In another aspect, the disclosure features a method for producing apolypeptide. The method comprises culturing the host cell (above) underconditions suitable for expression of the polypeptide encoded by thenucleic acid to thereby produce the polypeptide. The method can furtherinclude isolating the polypeptide from the host cell or media in whichthe host cell was cultured. Also featured herein is a polypeptideproduced using such a method.

In yet another aspect, the disclosure features any one of thepolypeptides described herein for use in the treatment of a conditionassociated with bone loss, lack of proper bone growth, lack of bonedensity, lack of bone strength, and the like. In some embodiments, thepolypeptides have a reduced or negligible secondary effect on musclegrowth and/or erythropoeisis (e.g., the polypeptides used at therapeuticlevels for treating the condition associated with bone loss do notappreciably increase muscle mass). The disclosure also features any oneor more of the polypeptides described herein for use in increasing bonegrowth, bone strength, or bone density in a subject (e.g., a human).

In another aspect, the disclosure features a method for increasing bonegrowth, bone strength, or bone density in a subject (e.g., a human). Themethod comprises administering to the subject in need thereof any one ofthe polypeptides described herein in an amount sufficient to increasebone growth, bone strength, or bone density in the subject. The subjectcan have a condition associated with bone loss, e.g., osteoporosis,Paget's disease, rheumatoid arthritis, a periodontal disease (e.g.,gingivitis or periodontitis), bone fracture, bone deficiency, metastaticbone disease, osteoarthritis, primary or secondary hyperparathyroidism,or osteolytic bone disease. The condition can also be any of thosedescribed herein or known in the art.

In some embodiments of any of the methods or uses described herein,following administration, the composition improves a bone parameter,such as one selected from the group consisting of bone volume density,total bone surface, bone surface density, trabecular number, trabecularthickness, trabecular spacing, and total volume. In some embodiments,any of the methods and uses described herein can further comprisemonitoring the subject for an improvement in any one of a number of boneparameters, such as: bone volume density, total bone surface, bonesurface density, trabecular number, trabecular thickness, trabecularspacing, or total volume.

In some embodiments of the treatment of bone disorders, polypeptidesthat home to bone (e.g., have bone-targeting moieties) are administeredto the subject.

In some embodiments, the polypeptide is administered to the subjectintravenously. In some embodiments, the polypeptide is administered tothe subject subcutaneously.

In some embodiments of any of the methods or uses described herein, thesubject is one who has failed another treatment for a conditionassociated with bone loss. The treatment can be a bisphosphonate oranother Activin A inhibitor (e.g., an Activin RIIA-IgG Fc fusion or anActivin Fc fusion).

In some embodiments, any of the methods or uses described herein canalso comprise administering to the subject at least one additionaltherapeutic agent that promotes bone growth or inhibits bone resorption.

In yet another aspect, the disclosure features a method for increasingmuscle mass or muscle strength in a subject in need thereof, whichmethod comprises administering to the subject one or more of any of thepolypeptides described herein in an amount sufficient to increase musclemass or muscle strength in the subject. In some embodiments, the subjectis one having a muscle disorder (e.g., a muscle wasting disorder).

In yet another aspect, the disclosure features a method for treating asubject having a muscle-wasting disorder or muscle atrophy. The methodcomprises administering to the subject one or more of any of thepolypeptides described herein in an amount sufficient to treat themuscle-wasting disorder or muscle atrophy.

In some embodiments, the muscle-wasting condition is, or is associatedwith, Duchenne muscular dystrophy (DMD), multiple types of limb girdleMD (LGMD), other congenital MDs (CMD), sarcopenia, cancer cachexia, orDiabetes mellitus.

In another aspect, the disclosure features a method for treating amusculoskeletal disorder in a subject. The method includes administeringto the subject one or more of any of the polypeptides described hereinin an amount sufficient to treat the musculoskeletal disorder. In someembodiments, the musculoskeletal disorder is osteoporosis, osteopenia,sarcopenia, arthritis, tissue atrophy, periodontal disease, woundhealing, or bone loss due to, e.g., malignancy, endocrine disorders,arthritis, immobility, or disuse.

In yet another aspect, the disclosure features a method for treating ametabolic condition, which method comprises administering to the subjectone or more of any of the polypeptides described herein in an amountsufficient to treat the metabolic disorder. The metabolic disorder canbe, e.g., type 2 diabetes, noninsulin-dependent diabetes mellitus,hyperglycemia, and obesity.

In another aspect, the disclosure features a method for treating asubject having an immune disorder (e.g., an inflammatory disease orautoimmune disorder). The method comprises administering to the subjectone or more of any of the polypeptides described herein in an amountsufficient to treat the immune disorder. In some embodiments, the immunedisorder is one associated with aberrant host defense response. In someembodiments, the immune disorder can be, e.g.: (a) acute injury oftissues inflicted by infection, toxic substances or trauma, woundhealing pursuant to surgery, severe burns or other tissue injury,meningitis, appendicitis, renal tubular necrosis, traumatic brain injuryand sepsis; (b) autoimmune diseases including, but not limited to,rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease,vasculitis, anti-phospholipid syndrome, scleroderma, systemic lupuserythematosous and osteoarthritis; and (c) respiratory diseasesincluding, but not limited to pneumonia, sarcoidosis, bronchiolitisobliterans, pulmonary hypertension, pneumonia, acute respiratorydistress syndrome, chronic obstructive pulmonary disease (COPD), acuteresponses against infectious agents such as pathogenic virusesincluding, but not limited to, influenza A viruses H5N1 and H1N1,coronaviruses SARS, and human rhinoviruses C and D.

In yet another aspect, the disclosure features a method for treating asubject having a cancer. The method comprises administering to thesubject one or more of any of the polypeptides described herein in anamount sufficient to treat the cancer. In some embodiments, the cancercomprises cancer cells that express one or more receptors for Activin Aor Activin B. In some embodiments, the proliferation and/or viability ofthe cancer cells is positively regulated by Activin A or Activin B. Insome embodiments, the methods described herein can include requestingthe results of a test to determine whether cancer cells of the cancerexpress one or more of the receptors or are responsive to Activin A orActivin B. In some embodiments, the methods can include performing thetest to determine whether cancer cells of the cancer express one or moreof the receptors or are responsive to Activin A or Activin B.

In some embodiments, the cancer is a lung cancer, breast cancer, coloncancer, pancreatic cancer, renal cancer, stomach cancer, liver cancer,bone cancer, hematological cancer, neural tissue cancer, melanoma,thyroid cancer, ovarian cancer, testicular cancer, prostate cancer,cervical cancer, vaginal cancer, or bladder cancer.

In yet another aspect, the disclosure features any one of thepolypeptides described herein for use in the treatment of a subject(e.g., a human) afflicted with muscle atrophy, a muscle wastingcondition, a metabolic disorder (such as any of those described herein),an immune disorder, or a musculoskeletal disorder.

“Polypeptide,” “peptide,” and “protein” are used interchangeably andmean any peptide-linked chain of amino acids, regardless of length orpost-translational modification.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this disclosure pertains. Preferred methods andmaterials are described below, although methods and materials similar orequivalent to those described herein can also be used in the practice ortesting of the presently disclosed methods and compositions. Allpublications, patent applications, patents, and other referencesmentioned herein are incorporated by reference in their entirety.

Other features and advantages of the present disclosure, e.g., methodsfor treating a condition associated with bone loss, will be apparentfrom the following description, the examples, and from the claims.

BRIEF DESCRIPTION OF THE SEQUENCES

SEQ ID NO:1 depicts an exemplary amino acid sequence for human Cryptic.

SEQ ID NO:2 depicts an exemplary amino acid sequence for human Crypticwithout the sequence of its signal peptide.

SEQ ID NO:3 depicts an exemplary amino acid sequence for human Crypticwithout the sequence of its signal peptide or C-terminal GPI anchorsequence.

SEQ ID NO:4 depicts an exemplary amino acid sequence for the lowhomology domain of human Cryptic.

SEQ ID NO:5 depicts an exemplary amino acid sequence for the EpidermalGrowth Factor (EGF) domain of human Cryptic.

SEQ ID NO:6 depicts an exemplary amino acid sequence for theCripto-FRL-1-Cryptic (CFC) domain of human Cryptic.

SEQ ID NO:7 depicts an exemplary amino acid sequence for a fragment of ahuman Cryptic polypeptide.

SEQ ID NO:8 depicts an exemplary amino acid sequence of a fragment ofhuman Cryptic containing the EGF and CFC domains.

SEQ ID NO:9 depicts an exemplary amino acid sequence for a fragment of ahuman Cryptic polypeptide.

SEQ ID NO:10 depicts the amino acid sequence for an exemplary fusionpolypeptide described herein.

SEQ ID NO:11 depicts an exemplary amino acid sequence of a Crypticpolypeptide expressed in Rhesus macaque.

SEQ ID NO:12 depicts an exemplary amino acid sequence of a Crypticpolypeptide expressed in mouse.

SEQ ID NO:13 depicts an exemplary amino acid sequence for the humaninhibin beta A chain.

SEQ ID NO:14 depicts an exemplary amino acid sequence for the FLAGepitope tag.

SEQ ID NO:15 depicts an exemplary amino acid sequence for apolyhistidine epitope tag.

SEQ ID NO:16 depicts an exemplary amino acid sequence for an influenzahemagglutinin epitope tag.

SEQ ID NO:17 depicts an exemplary amino acid sequence for a human IgG Fcconstant region.

SEQ ID NOs:18 depicts an amino acid sequence for an exemplary linkerpeptide.

SEQ ID NOs:19 and 20 depict amino acid sequences for an exemplaryfragments of human Cryptic.

SEQ ID NO:21 depicts an amino acid sequence of a human IgG1 Fc region.

SEQ ID NO:22 depicts the amino acid sequence of an exemplary Cryptic-Fcfusion protein.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 consists of three panels: panel (A), panel (B), and panel (C),which depict construct design and fusion protein purification. In panelA, a multiple sequence alignment of human and mouse Cryptic and Cripto-1is shown. Both molecules have a signal peptide for secretion (not shownin the alignment), a Low Homology domain (teal), an EGF-like domain(orange), a CFC-domain (grey), and a GPI signal peptide (represented bythe purple box). The Cripto-1 GPI signal peptide is cleaved after Ser169(residues in yellow box). Cryptic of primate origin has a large,non-canonical GPI signal peptide and its GPI modified amino acid is notknown. For expression constructs, Cripto-1 and Cryptic were truncated atthe ‘FC-Fusion site’ (light blue). Panel B depicts the domainorganization of Cryptic and Cripto-1 constructs, which are colored as inA. Both molecules were fused to human Igg1-Fc via a 22 amino acid linkerat the ‘FC-Fusion site’. Panel C of FIG. 1 related to Cryptic-Fc andCripto-1-Fc expressed in CHO cells. Both molecules migrate as a single,well-defined peak in a size exclusion chromatographic column. Themolecular weight of each protein corresponds to the dimeric species.Non-reducing and reducing SDS-PAGE gels show the disulfide linkeddimeric species and the reduced, monomeric species, respectively.Dimerization occurs via cysteines in the Fc region.

FIG. 2 depicts the results of ligand binding experiments, and consistsof panels A to F: (A) Binding of Activin A to Cryptic; (B) Binding ofActivin B to Cryptic; (C) Binding of GDF-8 to Cryptic; and (D) Bindingof GDF-11 to Cryptic. (A-D) Cryptic-Fc was immobilized on the sensorchip and various concentrations of ligand as shown were injected. Curvefit of kinetic analysis is shown as orange lines. Panel E depicts thesuperposition of ligand binding to Cryptic. Panel F depicts thesuperposition of ligand binding to Cripto-1. (E-F) Cryptic-Fc andCripto-1-Fc were captured on the sensor chip and all ligands as shownwere injected at a concentration of 80 nM. Tested ligands includedActivin A, Activin B, GDF-8, GDF-11, Nodal, BMP-9, BMP-2, BMP-4, TGFβ-1,GDF-1, GDF-3. Commercially purchased Nodal, GDF-11 and GDF-3 areproduced by refolding from E. coli and might not be adequatelyfunctional. For example, Nodal shows significant lot variability.

FIG. 3 depicts the results of receptor interaction experiments andconsists of panels A, B, C, and D. Panel A depicts the binding ofCryptic to TGF-β family receptors. Type I receptors ALK4-Fc, andALK5-Fc, and type II receptors ACTRIIA-Fc, ACTRIIB-Fc, BMPRII-Fc, andTGF-βRII-Fc were captured on the sensor chip. Fc free Cryptic wasinjected at a concentration of 20 μM. Panel B depicts the binding ofActivin A to ALK4. ALK4-Fc was captured on the sensor chip and differentconcentrations of Activin A as shown were injected. Curve fit of kineticanalysis is shown as orange lines. Panel C depicts the binding ofActivin A/Cryptic complexes to ALK4. ALK4-Fc was captured on the sensorchip and 10 nM Activin A preincubated with Fc free Cryptic (0-40 nM)were injected. The increase in response units when binding Cryptic iscaused by a higher molecular weight of the Activin A-Cryptic complex.Saturation is dependent only on the concentration of Activin A. Panel Ddepicts the binding of Activin A/Cryptic complexes to ALK4. ALK4-Fc wascaptured on the sensor chip and different concentrations of Activin A asshown preincubated with a constant amount of Fc free Cryptic (400 nM)were injected.

FIG. 4 depicts the results of competitive inhibition studies andconsists of panels A to H. Panel A depicts inhibition of Activin Abinding to ACTRIIA by Cryptic. Panel B depicts inhibition of Activin Abinding to ACTRIIB by Cryptic. (A-B) ACTRIIA-Fc or ACTRIIB-Fc werecaptured on the sensor chip and 1 nM Activin A preincubated with 0 nM,0.5, nM, 5 nM, 10 nM or 40 nM Fc-free Cryptic was injected. Panel Cdepicts the inhibition of Activin B binding to ACTRIIA by Cryptic. PanelD depicts the inhibition of Activin B binding to ACTRIIB by Cryptic.Panel E depicts inhibition by Cryptic of GDF-8 binding to ACTRIIA. PanelF depicts the inhibition of GDF-8 binding to ACTRIIB by Cryptic. (C-F)ACTRIIA-Fc or ACTRIIB-Fc were captured on the sensor chip and 10 nMActivin B or GDF-8 preincubated with 0 nM, 5 nM, 50 nM 100 nM, 400 nM,800 nM, or 1600 nM Fc-free Cryptic was injected. Panel G depicts theinhibition by Cryptic of Activin B binding to BMPRII. BMPRII-Fc wascaptured on the sensor chip and 10 nM Activin B preincubated with 0 nM,5 nM, 50 nM 100 nM or 400 nM Fc-free Cryptic was injected. The smallinsert shows the sensogram of Activin B binding to BMPRII withsuperimposed curve fit. Panel H depicts the inhibition by ACTRIIA ofActivin A binding to Cryptic. Cryptic-Fc was captured on the sensor chipand 10 nM Activin A preincubated with 0 nM, 5 nM, 50 nM 100 nM or 400 nMFc-free Cryptic was injected.

FIG. 5 depicts the results of in vitro studies related toCryptic-mediated regulation of Activin signaling, and consists of panelsA to F. Panel A depicts Cryptic-Fc's suppression of Activin A-mediatedgene expression. 10 ng/ml Activin A induces expression of aSmad-2/3-responsive reporter. ACTRIIA-Fc and Cryptic-Fc equivalentlyinhibit the Activin A dependent luciferase signal in a concentrationdependent manner (shown in ng/ml). Panel B is a Western blot depictingthe detection of Smad2 phosphorylation. Activin A (10 ng/ml) inducesSmad2 phosphorylation. ACTRIIA-Fc and Cryptic-Fc prevent Activin Amediated Smad-2 phosphorylation equivalently in a concentrationdependent manner (1:10, 2:500, 3:10,000 ng/ml). Panel C depictsCryptic-Fc suppression of Activin B-mediated gene expression. 10 ng/mlActivin A induces expression of a Smad-2/3-responsive reporter.ACTRIIA-Fc and Cryptic-Fc equivalently inhibit the Activin B dependentluciferase signal in a concentration dependent manner (shown in ng/ml).Panel D is a Western blot depicting the detection of Smad2phosphorylation. Activin B (10 ng/ml) induces Smad2 phosphorylation.ACTRIIA-Fc and Cryptic-Fc prevent Activin B mediated Smad-2phosphorylation equivalently in a concentration dependent manner (1:10,2:500, 3:10,000 ng/ml). Panel E depicts the effect of Cryptic on ActivinA inhibition of osteoblast mineralization. HOS cells were cultured inthe presence of osteogenic medium with and without Activin A andCryptic-Fc. Mineralization was visualized by Alizarin Red S staining.Panel F depicts quantification of mineralization. Values are expressedas a % of mineralization in control wells.

FIG. 6 depicts molecular models in panels A to D. Panel A is a model ofligand-receptor interactions based on the BMP-9-ALK1-ACTRIIB structure.The disulfide linked homodimeric ligand (center, orange) binds theextracellular domains of type I Activin receptor-like kinases (lightblue) and type II Activin and BMP receptors (dark blue). Panel B is amodel of Cripto-1/Cryptic ligand interactions. Cripto-1 and Cryptic arecompetitive inhibitors of the type II Activin and BMP receptorinteraction, indicating that the binding site for Cripto-1 and Crypticon the ligand is the same as that the binding site for ACTRIIA, ACTRIIBand BMPRII. Panel C is a surface model of TGF-ß family signaling.Simultaneous binding of Ligand to both type I and type II receptorsinitiates a phosphorylation cascade that leads to translocation ofphosphorylated R-SMAD (light green) transcription factors to the nucleusand expression of target genes. Panel D is a cell surface model ofCripto-1/Cryptic function. Cripto-1 and Cryptic prevent binding of typeII receptors to the ligand, blocking the canonical TGF-β familysignaling-cascade.

FIG. 7 depicts a model of Cryptic-Fc (a Cryptic polypeptide fused to anIg Fc region) inhibition of Activin A in bone remodeling. Activin Asignals by binding type II Activin receptors (ActRIIA and ActRIIB)Cryptic-Fc prevents binding of Activin A to type II Activin receptors,and thus inhibits Activin A signaling, releasing the osteoinhibitoryeffect of Activin A and enabling osteoinduction by other TGFβ familysignaling molecules.

FIG. 8 depicts a series of fusion protein constructs, each comprisingall or a portion of Cryptic protein and highlighted the domaincomposition of Cryptic. Cryptic consists of a signal peptide forsecretion (SP), a Low homology domain (LH-D), an EGF domain (EGF), acanonical CFC-domain (CFC) and a carboxy-terminal GPI signal. ForCryptic-Fc, the extracellular domain of Cryptic lacking the GPI signalpeptide is fused to the Fc portion from human IgG1 via a 22 amino acidlinker.

DETAILED DESCRIPTION

The disclosure relates to, among other things, polypeptides, nucleicacids encoding the polypeptides, production of the polypeptides, and useof the polypeptides in various applications, such as diagnostic andtherapeutic methods. For example, the polypeptides are useful fortreating a subject having a condition associated with bone loss, acancer, a metabolic disorder (e.g., a disorder associated withinsufficient insulin production), an immune disorder, a muscle wastingcondition, or a musculoskeletal disorder. While in no way intended to belimiting, exemplary polypeptides, compositions containing thepolypeptides (e.g., pharmaceutical compositions and formulations), andmethods for making and using any of the foregoing are elaborated onbelow.

Polypeptides

The polypeptides described herein include a Cryptic polypeptide (e.g., avertebrate Cryptic polypeptide), a functional fragment thereof, or avariant of the polypeptide or fragment. In some embodiments, apolypeptide described herein includes all or part of a human Crypticpolypeptide, e.g., one comprising the amino acid sequence:

(SEQ ID NO: 1) MTWRHHVRLLFTVSLALQIINLGNSYQREKHNGGREEVTKVATQKHRQSPLNWTSSHFGEVTGSAEGWGPEEPLPYSRAFGEGASARPRCCRNGGTCVLGSFCVCPAHFTGRYCEHDQRRSECGALEHGAWTLRACHLCRCIFGALHCLPLQTPDRCDPKDFLASHAHGPSAGGAPSLLLLLPCALLHRLLRPDAPAHPRSLVPSVLQRERRPCGRPGLGHRL (UniProt Id. No. P0CG37).

In some embodiments, a polypeptide described herein includes all or partof a Cryptic polypeptide from any vertebrate, e.g., a reptile, a bird,or a mammal (e.g., a non-human mammal, such as a non-human primate(e.g., Rhesus macaque or Cynomolgus macaque)). Skilled artisans wouldappreciate that such sequences are known in the art or easily obtainableusing routine experimentation (see, e.g., Sambrook et al. (infra)). Insome embodiments, the polypeptide comprises all or part of a Crypticpolypeptide from Pan troglodytes, e.g., having the following amino acidsequence:

(SEQ ID NO: 11) MTWRHHVRLLFTVSLALQIINLGNSYQREKHNGGREEVIKVATQKHQQSPLNWTSSHFGEVTGSAEGWGPEEPLTYSWAFGEGASARPRCCRNGGTCVLGSFCVCPAHFTGRYCEHDQRRSECGALEHGAWTLRACHLCRCIFGALHCLPLQTPDRCDPKDFLASHAHGPSAGGAPSLLLLLPCALLHRLLRPDAPAHPRSLVPSVLQRERRPCGRPGLGHRL (UniProt Id. No. H2QIQ5).

In some embodiments, a polypeptide described herein includes all or partof a rodent Cryptic polypeptide. For example, the polypeptide caninclude all or part of a murine Cryptic polypeptide, e.g., having thefollowing amino acid sequence:

(SEQ ID NO: 12) MRANSPTQGISLKMHQARPLFLVTVALQLIGLGYSYQSEGDGAREVSNILSPVIPGTTLDRTLSNSSRKNDIPEGARLWDSLPDSSTLGESAVPVSRCCHNGGTCVLGSFCVCPAYFTGRYCEHDQRRRDCGALGHGAWTLHSCRLCRCIFSALYCLPHQTFSHCDLKSFLSSGARGSECSIPSLLLLVLCLLLQGVAGKG (UniProt Id. No. P97766);

In some embodiments, a polypeptide described herein comprises thefollowing amino acid sequence:

(SEQ ID NO: 2) YQREKHNGGREEVTKVATQKHRQSPLNWTSSHFGEVTGSAEGWGPEEPLPYSRAFGEGASARPRCCRNGGTCVLGSFCVCPAHFTGRYCEHDQRRSECGALEHGAWTLRACHLCRCIFGALHCLPLQTPDRCDPKDFLASHAHGPSAGGAPSLLLLLPCALLHRLLRPDAPAHPRSLVPSVLQRERRPCGRPGLGHRL,which corresponds to the amino acid sequence of a human Crypticpolypeptide lacking the amino-terminal leader sequence. In someembodiments, a polypeptide described herein comprises the followingamino acid sequence:

(SEQ ID NO: 3) YQREKHNGGREEVTKVATQKHRQSPLNWTSSHFGEVTGSAEGWGPEEPLPYSRAFGEGASARPRCCRNGGTCVLGSFCVCPAHFTGRYCEHDQRRSECGALEHGAWTLRACHLCRCIFGALHCLPLQTPDRC,which corresponds to the amino acid sequence of a human Crypticpolypeptide without the amino-terminal leader sequence or thecarboxy-terminal pro-peptide domain.

In some embodiments, a polypeptide described herein comprises thefollowing amino acid sequence:

(SEQ ID NO: 4) YQREKHNGGREEVTKVATQKHRQSPLNWTSSHFGEVTGSAEGWGPEEPLPYSRAFGEGASAR,which corresponds to the low homology domain of a human Crypticpolypeptide. In some embodiments, a polypeptide described hereincomprises the EGF domain of a Cryptic polypeptide, e.g., the EGF domainof a human Cryptic polypeptide, e.g., comprising the following aminoacid sequence:

(SEQ ID NO: 5) PRCCRNGGTCVLGSFCVCPAHFTGRYCEHDQR,which corresponds to the EGF domain of a human Cryptic polypeptide. Insome embodiments, a polypeptide described herein comprises theCripto-FRL-1-Cryptic (CFC) domain of a Cryptic polypeptide, e.g., theCFC domain of a human Cryptic polypeptide, e.g., comprising thefollowing amino acid sequence:

(SEQ ID NO: 6) RSECGALEHGAWTLRACHLCRCIFGALHCLPLQTPDRCDPKDFLASHA.

In some embodiments, a polypeptide described herein comprises one ormore of the following amino acid sequences:

(SEQ ID NO: 7) CCRNGGTCVLGSFCVCPAHFTGRYCEHDQR, (SEQ ID NO: 8)PRCCRNGGTCVLGSFCVCPAHFTGRYCEHDQRRSECGALEHGAWTLRACHLCRCIFGALHCLPLQTPDRCDPKDFLASHA, or (SEQ ID NO: 9) NGGTCVLGSFC.A diagram of exemplary fragments of Cryptic are set forth in FIG. 8.

In some embodiments, a polypeptide described herein comprises one orboth of the following sequences:

(SEQ ID NO: 19) MTWRHHVRLL FTVSLALQII NLGNSYQREK HNGGREEVTK VATQKHRQSP LNWTSSHFGE VTGSAEGWGP EEPLPYSRAFGEGASARPRC CRNGGTCVLG SFCVCPAHFT GRYCEHDQRRSECGALEHGA WTLRACHLCR CIFGALHCLP LQTPDRCDPK  or (SEQ ID NO: 20)YQREK HNGGREEVTK  VATQKHRQSP LNWTSSHFGE VTGSAEGWGP EEPLPYSRAFGEGASARPRC CRNGGTCVLG SFCVCPAHFT GRYCEHDQRRSECGALEHGA WTLRACHLCR CIFGALHCLP LQTPDRCDPK. 

Also featured herein are polypeptides comprising variant Crypticpolypeptides, or fragments of the variant Cryptic polypeptides. Suchvariants comprise one or more amino acid substitutions, insertions, ordeletions, relative to the wild-type Cryptic polypeptides from whichthey were derived. In some embodiments, a variant polypeptide comprisesat least two (e.g., at least three, four, five, six, seven, eight, nine,10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95,100, or more than 100) amino acid substitutions, deletions, orinsertions, relative to the wild-type Cryptic polypeptide from which itwas derived (e.g., a wild-type human Cryptic polypeptide comprising theamino acid sequence depicted in SEQ ID NO:2 or 3). In some embodiments,a variant polypeptide comprises no more than 20 (e.g., no more than 19,18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, or 2) aminoacid substitutions, deletions, or insertions, relative to the wild-typeCryptic polypeptide from which it was derived (e.g., a wild-type humanCryptic polypeptide comprising the amino acid sequence depicted in SEQID NO:2 or 3). The substitutions can be conservative, non-conservative,or a mixture of both.

As used herein, the term “conservative substitution” refers to thereplacement of an amino acid present in the native sequence in a givenpolypeptide with a naturally or non-naturally occurring amino acidhaving similar steric properties. Where the side-chain of the nativeamino acid to be replaced is either polar or hydrophobic, theconservative substitution should be with a naturally occurring aminoacid, a non-naturally occurring amino acid that is also polar orhydrophobic, and, optionally, with the same or similar steric propertiesas the side-chain of the replaced amino acid. Conservative substitutionstypically include substitutions within the following groups: glycine andalanine; valine, isoleucine, and leucine; aspartic acid and glutamicacid; asparagine, glutamine, serine and threonine; lysine, histidine andarginine; and phenylalanine and tyrosine. One letter amino acidabbreviations are as follows: alanine (A); arginine (R); asparagine (N);aspartic acid (D); cysteine (C); glycine (G); glutamine (Q); glutamicacid (E); histidine (H); isoleucine (I); leucine (L); lysine (K);methionine (M); phenylalanine (F); proline (P); serine (S); threonine(T); tryptophan (W), tyrosine (Y); and valine (V).

The phrase “non-conservative substitutions” as used herein refers toreplacement of the amino acid as present in the parent sequence byanother naturally or non-naturally occurring amino acid, havingdifferent electrochemical and/or steric properties. Thus, the side chainof the substituting amino acid can be significantly larger (or smaller)than the side chain of the native amino acid being substituted and/orcan have functional groups with significantly different electronicproperties than the amino acid being substituted.

In some embodiments, a polypeptide described herein comprises a variantCryptic polypeptide having an amino acid sequence that is at least 70(e.g., at least 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84,85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99) %identical to the wild-type Cryptic polypeptide from which it wasderived. For example, in some embodiments, a variant polypeptidedescribed herein, or a fragment thereof, has an amino acid sequence thatis at least 80 (e.g., at least 81, 82, 83, 84, 85, 86, 87, 88, 89, 90,91, 92, 93, 94, 95, 96, 97, 98, or 99) % identical to any one of theamino acid sequences depicted in SEQ ID NOs: 1 to 12.

In some embodiments, a polypeptide described herein comprises an aminoacid sequence that comprises any one (or more) of the following aminoacid sequences:

(SEQ ID NO: 4) YQREKHNGGREEVTKVATQKHRQSPLNWTSSHFGEVTGSAEGWGPEEPLPYSRAFGEGASAR, (SEQ ID NO: 5) PRCCRNGGTCVLGSFCVCPAHFTGRYCEHDQR,(SEQ ID NO: 6) RSECGALEHGAWTLRACHLCRCIFGALHCLPLQTPDRCDPKDFLASHA,(SEQ ID NO: 7) CCRNGGTCVLGSFCVCPAHFTGRYCEHDQR,  (SEQ ID NO: 8)PRCCRNGGTCVLGSFCVCPAHFTGRYCEHDQRRSECGALEHGAWTLRACHLCRCIFGALHCLPLQTPDRCDPKDFLASHA, or (SEQ ID NO: 9) NGGTCVLGSFC,wherein the amino acid sequence of the polypeptide is otherwise at least70 (e.g., at least 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99) %identical to the amino acid sequence depicted in SEQ ID NO: 1 or 2.

Percent (%) amino acid sequence identity is defined as the percentage ofamino acids in a candidate sequence that are identical to the aminoacids in a reference sequence, after aligning the sequences andintroducing gaps, if necessary, to achieve the maximum percent sequenceidentity. Alignment for purposes of determining percent sequenceidentity can be achieved in various ways that are within the skill inthe art, for instance, using publicly available computer software, suchas BLAST software or ClustalW2. Appropriate parameters for measuringalignment, including any algorithms needed to achieve maximal alignmentover the full-length of the sequences being compared can be determinedby known methods.

In some embodiments, a polypeptide described herein includes afunctional fragment of a Cryptic polypeptide or a variant Crypticpolypeptide. Such functional fragments, as well as variant polypeptides,retain at least 5 (e.g., at least 10, 15, 20, 25, 30, 35, 40, 45, 50,55, 60, 65, 70, 75, 80, 85, 90, 95, or 100) % of the activity of thecorresponding mature Cryptic polypeptide from which the variant orfragment was derived. For example, in some embodiments variants orfunctional fragments described herein retain at least 5 (e.g., at least10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95,or 100) % of the affinity of the mature, wild-type Cryptic polypeptidefrom which the variant or functional fragment was derived for Activin Aand/or Activin B.

The polypeptides described herein can specifically bind to Activin A(e.g., human Activin A). The terms “specific binding,” “specificallybinds,” and like grammatical terms, as used herein, refer to twomolecules forming a complex that is relatively stable under physiologicconditions. Typically, binding is considered specific when theassociation constant (k_(a)) is higher than 10⁶M⁻¹s⁻¹. Thus, apolypeptide described herein can specifically bind to Activin A with ak_(a) of at least (or greater than) 10⁶ (e.g., at least or greater than10⁷, 10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹², 10¹³, 10¹⁴, or 10¹⁵ or higher) M⁻¹s⁻¹.In some embodiments, a polypeptide described herein has a dissociationconstant (k_(d)) of less than or equal to 10⁻³ (e.g., 8×10⁻⁴, 5×10⁻⁴,2×10⁻⁴, 10⁻⁴, or 10⁻⁵) s⁻¹.

In some embodiments, a polypeptide described herein binds to Activin A(e.g., human Activin A) with a K_(D) of less than 10⁻⁸, 10⁻⁹, 10⁻¹⁰,10⁻¹¹, 10⁻¹² M, or 10⁻¹³M. The equilibrium constant K_(D) is the ratioof the kinetic rate constants—k_(d)/k_(a). In some embodiments, apolypeptide described herein binds to Activin A with a K_(D) of lessthan 1×10⁻⁹M. In some embodiments, a polypeptide described herein bindsto Activin A with a K_(D) of less than 100 picomolar, less than 50picomolar, less than 25 picomolar, less than 10 picomolar, or less than5 picomolar. In some embodiments, the polypeptide binds to Activin Awith a K_(D) that is between about 1 picomolar and about 100 picomolar,e.g., about 1 to about 5 picomolar, about 1 to about 10 picomolar, about1 to about 20 picomolar, or about 1 to about 50 picomolar.

In some embodiments, a polypeptide described herein binds to Activin B(e.g., human Activin B) with a K_(D) of less than 10⁻⁸, 10⁻⁹, or 5×10⁻¹⁰M. In some embodiments, a polypeptide described herein binds to ActivinB with a K_(D) of less than 1×10⁻⁹M. In some embodiments, a polypeptidedescribed herein binds to Activin B with a K_(D) of less than 500picomolar.

Methods for determining whether a polypeptide binds to a target antigenand/or the affinity for a polypeptide to a target antigen are known inthe art. For example, the binding of one polypeptide to a targetpolypeptide can be detected and/or quantified using a variety oftechniques such as, but not limited to, Western blot, dot blot, plasmonsurface resonance method (e.g., BIAcore system; Pharmacia Biosensor AB,Uppsala, Sweden and Piscataway, N.J.), or enzyme-linked immunosorbentassays (ELISA). Exemplary methods for evaluating the interaction of anagent and Activin A are described in, e.g., Li et al. (2010) J Biol Chem285(47):36645-36655; Harrington et al. (2006) EMBO J 25:1035-1045; andFischer et al. (2003) J Endocrinol 176:61-68, the disclosures of each ofwhich are incorporated herein by reference in their entirety.

The amino acid sequences for mature Activin A from several species(including human) are well known in the art. Human Activin A, forexample, is a homodimer of two 13 kDa inhibin βA subunits, which is notactive until the amino-terminal propeptide is cleaved from each of thesubunits. An exemplary amino acid sequence for the human inhibin beta Achain is as follows:

(SEQ ID NO: 13) MPLLWLRGFLLASCWIIVRS SPTPGSEGHSAAPDCPSCALAALPKDVPNSQPEMVEAVKKHILNMLHLKKRPDVTQPVPKAALLNAIRKLHVGKVGENGYVEIEDDIGRRAEMNELMEQTSEIITFAESGTARKTLHFEISKEGSDLSVVERAEVWLFLKVPKANRTRTKVTIRLFQQQKHPQGSLDTGEEAEEVGLKGERSELLLSEKVVDARKSTWHVFPVSSSIQRLLDQGKSSLDVRIACEQCQESGASLVLLGKKKKKEEEGEGKKKGGGEGGAGADEEKEQSHRPFLMLQARQSEDHPHRRRRRGLECDGKVNICCKKQFFVSFKDIGWNDWIIAPSGYHANYCEGECPSHIAGTSGSSLSFHSTVINHYRMRGHSPFANLKSCCVPTKLRPMSMLYYDDGQNIIKKDIQNMIVEECGCS (UniProt Id. No. P08476).Amino acids corresponding to the signal peptide are bolded and thosecorresponding to the propeptide are underlined.

Activin A has been described in the art and Activin A protein, which maybe used in any of the methods described herein, is commerciallyavailable from a number of sources, such as affymetrix eBioscience (SanDiego, Calif.) and R&D Systems (Minneapolis, Minn.).

In some embodiments, variants or functional fragments described hereinretain at least 5 (e.g., at least 10, 15, 20, 25, 30, 35, 40, 45, 50,55, 60, 65, 70, 75, 80, 85, 90, 95, or 100) % of the ability of themature, wild-type Cryptic polypeptide from which the variant orfunctional fragment was derived to inhibit the binding of Activin A toits cognate cellular surface receptor(s) and/or the ability of Activin Ato induce intracellular signaling through at least one of the cognatecell surface receptors for Activin A. Cell-based methods for evaluatingActivin A signaling (or inhibition thereof) are known in the art and aredescribed in, e.g., Harrington et al., supra, Schmierer et al. (2003) JBiol Chem 278:21197-21203; Chantry et al. (2010) J Bone Mineral Res25(12):2633-2646; and U.S. Patent Application Publication No.20120141469. For example, cultured osteoblasts can be contacted withActivin A in the presence or absence of a Cryptic polypeptide or avariant or functional fragment thereof. The extent of osteoblastmineralization can be measured. In addition, the effect of a testinhibitor (e.g., a variant or functional fragment of Cryptic describedherein) of Activin A on osteoclast number or activity can also bemeasured, e.g., as described in Chantry et al. (supra).

In some embodiments, variants or functional fragments described hereinretain at least 5 (e.g., at least 10, 15, 20, 25, 30, 35, 40, 45, 50,55, 60, 65, 70, 75, 80, 85, 90, 95, or 100) % of the ability of themature, wild-type Cryptic polypeptide from which the variant orfunctional fragment was derived to inhibit the binding of Activin B toits cognate cellular surface receptor(s) and/or the ability of Activin Bto induce intracellular signaling through at least one of the cognatecell surface receptors for Activin B. Cell-based methods for evaluatingActivin B signaling (or inhibition thereof) are known in the art and aredescribed in, e.g., Tsuchida et al. (2004) Mol Cell Endocrinol220(1-2):59-65; Wacker et al. (2014) PLoS One 9(10):e111276; Frandsen etal. (2007) Biochem Biophys Res Commun 362(3):568-574; and U.S. Pat. No.5,071,834.

As used herein, the term “inhibiting” and grammatical equivalentsthereof refer to a decrease, limiting, and/or blocking of a particularaction, function, or interaction. In one embodiment, the term refers toreducing the level of a given output or parameter to a quantity which isat least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 99% or less than the quantity in acorresponding control. A reduced level of a given output or parameterneed not, although it may, mean an absolute absence of the output orparameter. The invention does not require, and is not limited to,methods that wholly eliminate the output or parameter.

In some embodiments, variants or functional fragments described hereinretain at least 5 (e.g., at least 10, 15, 20, 25, 30, 35, 40, 45, 50,55, 60, 65, 70, 75, 80, 85, 90, 95, or 100) % of the affinity of themature, wild-type Cryptic polypeptide from which the variant orfunctional fragment was derived to inhibit the interaction of Activin Aand/or Activin B with one of its cognate cellular receptors (e.g.,ActRIIA or ActRIIB).

As used herein, the term “interaction”, when referring to an interactionbetween two molecules, refers to the physical contact (e.g., binding) ofthe molecules with one another. Generally, such an interaction resultsin an activity (which produces a biological effect) of one or both ofsaid molecules. To inhibit such an interaction results in the disruptionof the activity of one or more molecules involved in the interaction.Inhibition can, but need not, be complete.

Functionally active variants or fragments can be obtained by screeningpolypeptides recombinantly produced (see below). In addition, fragmentscan be chemically synthesized using techniques well known in the art,such as solid phase f-Moc or t-Boc chemistry. The fragments can beproduced (recombinantly or by chemical synthesis) and tested to identifythose peptidyl fragments that can function as antagonists (inhibitors)of Activin A protein or signaling mediated by Activin A (and/or ActivinB protein or signaling mediated by Activin B). Functionally activevariants of a polypeptide can also be obtained by screening libraries ofmodified polypeptides recombinantly produced from the correspondingmutagenized nucleic acids encoding a Cryptic polypeptide. The variantscan be produced and tested to identify those that can function asantagonists (inhibitors) of Activin A protein (or Activin B) orsignaling mediated by Activin A (or Activin B).

A combinatorial library may be produced by way of a degenerate libraryof genes encoding a library of polypeptides which each include at leasta portion of Cryptic polypeptide sequences. For instance, a mixture ofsynthetic oligonucleotides can be enzymatically ligated into genesequences such that the degenerate set of potential Cryptic polypeptidenucleotide sequences are expressible as individual polypeptides, oralternatively, as a set of larger fusion proteins (e.g., for phagedisplay).

There are many ways by which the library of potential homologs can begenerated from a degenerate oligonucleotide sequence. Chemical synthesisof a degenerate gene sequence can be carried out in an automatic DNAsynthesizer, and the synthetic genes then be ligated into an appropriatevector for expression. The synthesis of degenerate oligonucleotides iswell known in the art (see for example, Narang (1983) Tetrahedron 39:3;Itakura et al. (1984) Annu Rev Biochem 53:323; Itakura et al. (1984)Science 198:1056; and Ike et al. (1983) Nucleic Acid Res 11:477). Suchtechniques have been employed in the directed evolution of otherproteins (see, for example, Scott et al. (1990) Science 249:386-390;Roberts et al. (1992) Proc Natl Acad Sci USA 89:2429-2433; Devlin et al.(1990) Science 249: 404-406; Cwirla et al. (1990) Proc Natl Acad Sci USA87: 6378-6382; as well as U.S. Pat. Nos. 5,223,409; 5,198,346; and5,096,815).

A wide range of techniques are known in the art for screening geneproducts of combinatorial libraries made by point mutations andtruncations, and, for that matter, for screening cDNA libraries for geneproducts having a certain property. Such techniques will be generallyadaptable for rapid screening of the gene libraries generated by thecombinatorial mutagenesis of Cryptic polypeptides. The most widely usedtechniques for screening large gene libraries typically comprisescloning the gene library into replicable expression vectors,transforming appropriate cells with the resulting library of vectors,and expressing the combinatorial genes under conditions in whichdetection of a desired activity facilitates relatively easy isolation ofthe vector encoding the gene whose product was detected. Preferredassays include activin binding assays and activin-mediated cellsignaling assays.

In some embodiments, a polypeptide described herein can be conjugated toa heterologous moiety. The heterologous moiety can be, e.g., aheterologous polypeptide, a therapeutic agent (e.g., a toxin or a drug),or a detectable label such as, but not limited to, a radioactive label,an enzymatic label, a fluorescent label, a heavy metal label, aluminescent label, or an affinity tag such as biotin or streptavidin.Suitable heterologous polypeptides include, e.g., an antigenic tag(e.g., FLAG (DYKDDDDK (SEQ ID NO:14)), polyhistidine (6-His; HHHHHH (SEQID NO:15), hemagglutinin (HA; YPYDVPDYA (SEQ ID NO:16)),glutathione-S-transferase (GST), or maltose-binding protein (MBP)) foruse in purifying the antibodies or fragments. Heterologous polypeptidesalso include polypeptides (e.g., enzymes) that are useful as diagnosticor detectable markers, for example, luciferase, a fluorescent protein(e.g., green fluorescent protein (GFP)), or chloramphenicol acetyltransferase (CAT). Suitable radioactive labels include, e.g., ³²P, ³³P,¹⁴C, ¹²⁵I, ¹³¹I, ³⁵S, and ³H. Suitable fluorescent labels include,without limitation, fluorescein, fluorescein isothiocyanate (FITC),green fluorescent protein (GFP), DyLight™ 488, phycoerythrin (PE),propidium iodide (PI), PerCP, PE-Alexa Fluor® 700, Cy5, allophycocyanin,and Cy7. Luminescent labels include, e.g., any of a variety ofluminescent lanthanide (e.g., europium or terbium) chelates. Forexample, suitable europium chelates include the europium chelate ofdiethylene triamine pentaacetic acid (DTPA) ortetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA). Enzymatic labelsinclude, e.g., alkaline phosphatase, CAT, luciferase, and horseradishperoxidase.

Two proteins can be cross-linked using any of a number of known chemicalcross linkers. Examples of such cross linkers are those which link twoamino acid residues via a linkage that includes a “hindered” disulfidebond. In these linkages, a disulfide bond within the cross-linking unitis protected (by hindering groups on either side of the disulfide bond)from reduction by the action, for example, of reduced glutathione or theenzyme disulfide reductase. One suitable reagent,4-succinimidyloxycarbonyl-α-methyl-α(2-pyridyldithio) toluene (SMPT),forms such a linkage between two proteins utilizing a terminal lysine onone of the proteins and a terminal cysteine on the other.Heterobifunctional reagents that cross-link by a different couplingmoiety on each protein can also be used. Other useful cross-linkersinclude, without limitation, reagents which link two amino groups (e.g.,N-5-azido-2-nitrobenzoyloxysuccinimide), two sulfhydryl groups (e.g.,1,4-bis-maleimidobutane), an amino group and a sulfhydryl group (e.g.,m-maleimidobenzoyl-N-hydroxysuccinimide ester), an amino group and acarboxyl group (e.g., 4-[p-azidosalicylamido]butylamine), and an aminogroup and a guanidinium group that is present in the side chain ofarginine (e.g., p-azidophenyl glyoxal monohydrate).

In some embodiments, a radioactive label can be directly conjugated tothe amino acid backbone of a protein agent. Alternatively, theradioactive label can be included as part of a larger molecule (e.g.,¹²⁵I in meta-[¹²⁵I]iodophenyl-N-hydroxysuccinimide ([¹²⁵I]mIPNHS) whichbinds to free amino groups to form meta-iodophenyl (mIP) derivatives ofrelevant proteins (see, e.g., Rogers et al. (1997) J Nucl Med38:1221-1229) or chelate (e.g., to DOTA or DTPA) which is in turn boundto the protein backbone. Methods of conjugating the radioactive labelsor larger molecules/chelates containing them to the antibodies orantigen-binding fragments described herein are known in the art. Suchmethods involve incubating the proteins with the radioactive label underconditions (e.g., pH, salt concentration, and/or temperature) thatfacilitate binding of the radioactive label or chelate to the protein(see, e.g., U.S. Pat. No. 6,001,329).

Methods for conjugating a fluorescent label (sometimes referred to as a“fluorophore”) to a protein (e.g., an antibody) are known in the art ofprotein chemistry. For example, fluorophores can be conjugated to freeamino groups (e.g., of lysines) or sulfhydryl groups (e.g., cysteines)of proteins using succinimidyl (NETS) ester or tetrafluorophenyl (TFP)ester moieties attached to the fluorophores. In some embodiments, thefluorophores can be conjugated to a heterobifunctional cross-linkermoiety such as sulfo-SMCC. Suitable conjugation methods involveincubating an antibody protein, or fragment thereof, with thefluorophore under conditions that facilitate binding of the fluorophoreto the protein. See, e.g., Welch and Redvanly (2003) “Handbook ofRadiopharmaceuticals: Radiochemistry and Applications,” John Wiley andSons (ISBN 0471495603).

In some embodiments, the agents can be modified, e.g., with a moietythat improves the stabilization and/or retention of the antibodies incirculation, e.g., in blood, serum, or other tissues. For example, anagent comprising a Cryptic polypeptide, or variant or functionalfragment thereof, can be PEGylated as described in, e.g., Lee et al.(1999) Bioconjug Chem 10(6): 973-8; Kinstler et al. (2002) Advanced DrugDeliveries Reviews 54:477-485; and Roberts et al. (2002) Advanced DrugDelivery Reviews 54:459-476 or HESylated (Fresenius Kabi, Germany; see,e.g., Pavisić et al. (2010) Int J Pharm 387(1-2):110-119). Thestabilization moiety can improve the stability, or retention of, thepolypeptide by at least 1.5 (e.g., at least 2, 5, 10, 15, 20, 25, 30,40, or 50 or more) fold.

In some embodiments, the polypeptides described herein may contain abone targeting agent. Agents which have an affinity for bone or anability to home to bone are known in the art. As used herein, a “bonetargeting agent” refers to a chemical structure or ligand that has ahigh affinity for calcium ions in hydroxyapatite, the major constituentof bone. Polypeptides can be targeted, in an embodiment, to calciumdeposits in regions of the body other than bone, such as calciumdeposits in the arteries, heart, kidney, or gall bladder. However, thebone targeting agent ideally selectively binds to bone tissue. A bonetargeting agent is attracted to the bone tissue of the subject,preferably binds to the bone with a higher affinity than non-bonetissues, and remains bound for a certain length of time therebydelivering the composition to a bone environment. In other words, thebone targeting agent preferably binds to bone tissue with at least2-fold greater affinity (e.g., at least 3-fold, at least 5-fold, atleast 10-fold, or at least 25-fold greater affinity) than to a non-bonetissue. The bone targeting agent preferably reversibly binds to bonetissue, meaning that the bone targeting agent is eventually releasedfrom bone and expelled from the body.

In some embodiments, the bone targeting agent desirably is selected fromthe group consisting of a phosphate, a phosphonate, a bisphosphonate, ahydroxybisphosphonate, an aminomethylenephosphonic acid, an acidicpeptide, or a combination thereof. The bone targeting agent can carryone, two, three, or more of these groups. For example, the bonetargeting agent can be a phosphonate, meaning that the bone targetingagent may comprise one phosphonate, two phosphonates, or three or morephosphonates. One suitable bone targeting agent for use in the inventionis EDTMP (ethylene diamine-N,N,N′,N′-tetrakis(methylenephosphonic acid),currently FDA approved (Quadramet™) as the radioactive ¹⁵³Sm complex fordelivering a selective radiation dose to bone metastases for painpalliation. EDTMP is a phosphonate that contains four phosphonic acidgroups, and is therefore a tetraphosphonate. Compounds, such as¹⁵³Sm-EDTMP are selectively localized in bone where tumors are presentversus normal bone in a ratio of more than 10:1.

In some embodiments, the bone targeting agent is a polyphosphonic acid.Polyphosphonic acid has been demonstrated to successfully targetbiologically-active molecules to bone tissue. For example, conjugation(via isothiocyanato chemistry) of polyaminophosphonic acids, such asABDTMP, to growth factors (to stimulate bone formation) successfullyresulted in the targeting of the growth factors to the bones of rats(see, for example, International Patent Application Publication WO94/00145). Similarly, bone targeting agents have been coupled toproteins. For example bisphosphonates that were conjugated to humanserum albumin successfully delivered the protein to bone in vitro(Biotechnol Prog 16:258 (2000)) and in vivo (Biotechnol Prog 16:1116(2000)). The utility of bone targeting agents extends beyond delivery ofproteins to bone and includes, for instance, small therapeuticmolecules. A conjugate comprising a bone targeting bisphosphonate and analkylating agent, such as BAD has been generated (see, for example,Wingen et al. (1986) J Cancer Res Clin Oncol 111:209).

In some embodiments, the bone targeting agent comprises the formula:X_(n), wherein X is a canonical or noncanonical amino acid that has anegative charge at physiological pH and n is an integer from 1 to 25. Insome embodiments, X is aspartic acid or glutamic acid. In someembodiments, n is an integer between 5 and 15. In some embodiments, n isan integer between 10 and 16. In some embodiments, n is at least 4(e.g., at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,or 20). In some embodiments, n is less than 20 (e.g., less than 19, 18,17, 16, or 15).

In other embodiments, the bone targeting agent is (aspartic acid)_(n) or(glutamic acid)_(n). The acid-rich peptide sequence of the glycoproteinosteonectin, which is found in abundance in bone and dentin, has astrong affinity to hydroxyapatite (Fujisawa et al. (1996) Biochimica etBiophysica Acta 53:1292). Thus, peptide ligands comprising acidic aminoacids are suitable candidates for bone targeting agents. Indeed,(Glu)₁₀, when attached to biotin, successfully recruited labeledstreptavidin to hydroxyapatite (described further in InternationalPatent Application Publication No. WO 98/35703). It is believed that the(Asp)₆ tether to bone is metabolized during the bone resorption processmediated by osteoclasts. Therefore, the acidic peptide ligand providesnot only a means of recruiting compounds to bone, but also provides amechanism of slowly releasing compounds to bone cells and surroundingtissue.

Other examples of bone targeting agents include, but are not limited toamino- and hydroxy-alkyl phosphonic and diphosphonic acids;hydroxybisphosphonic acids including alendronate, pamidronate,4-aminobutylphosphonic acid, 1-hydroxyethane-1,1-diphosphonic acid, andaminomethylenebisphosphonic acid; phosphates such as phytic acid; andaminomethylenephosphonic acids such asN,N-bis(methylphosphono)-4-amino-benzoic acid andnitrilotri(methylphosphonic acid).

In some embodiments, e.g., embodiments in which the bone-targeting agentis a protein, the agent can be part of the polypeptides described hereinas a fusion protein (see below).

Fusion Proteins

In some embodiments, the polypeptides can be fusion proteins having atleast a portion of the Cryptic polypeptides (also variants or functionalfragments of the Cryptic peptides) and one or more fusion domains. Wellknown examples of such fusion domains include, but are not limited to,polyhistidine, Glu-Glu, glutathione S transferase (GST), thioredoxin,protein A, protein G, an immunoglobulin heavy chain constant region(Fc), maltose binding protein (MBP), or human serum albumin. A fusiondomain may be selected so as to confer a desired property. For example,some fusion domains are particularly useful for isolation of the fusionproteins by affinity chromatography. For the purpose of affinitypurification, relevant matrices for affinity chromatography, such asglutathione-, amylase-, and nickel- or cobalt-conjugated resins areused. As another example, a fusion domain may be selected so as tofacilitate detection of the polypeptides. Examples of such detectiondomains include the various fluorescent proteins (e.g., GFP) as well as“epitope tags,” which are usually short peptide sequences for which aspecific antibody is available. Well known epitope tags for whichspecific monoclonal antibodies are readily available include FLAG,influenza virus haemagglutinin (HA), and c-myc tags. In someembodiments, the fusion proteins comprise a linker moiety of one or moreamino acids separating the Cryptic polypeptide (variant or functionalfragment) portion and the heterologous portion (e.g., the Fc region oralbumin molecule). In some embodiments, the linker moiety comprises theamino acid sequence depicted in SEQ ID NO:18 (ENLYFQGGGSGGSGGDYKDDDD).In some embodiments, the linker region comprises a polyglycine sequenceor poly (GS) sequence. In some cases, the fusion domains have a proteasecleavage site, such as for Factor Xa, Thrombin, or Tobacco Etch Virus(TEV) protease, which allows the relevant protease to partially digestthe fusion proteins and thereby liberate the recombinant proteinstherefrom. The liberated proteins can then be isolated from the fusiondomain by subsequent chromatographic separation. In some embodiments, anCryptic polypeptide can be fused with a domain that stabilizes theCryptic polypeptide in vivo (a “stabilizer” domain). By “stabilizing” ismeant anything that increases serum half-life, regardless of whetherthis is because of decreased destruction, decreased clearance by thekidney, or other pharmacokinetic effect. Fusions with the Fc portion ofan immunoglobulin are known to confer desirable pharmacokineticproperties on a wide range of proteins. Likewise, fusions to human serumalbumin can confer desirable properties. Other types of fusion domainsthat may be selected include multimerizing (e.g., dimerizing,tetramerizing) domains and functional domains (that confer an additionalbiological function, such as further stimulation of bone growth, asdesired).

In some embodiments, the fusion protein can comprise a Crypticpolypeptide (or a variant or functional fragment thereof) fused to an Fcdomain. In some embodiments, the Fc domain can comprise or consist ofthe following amino acid sequence:

(SEQ ID NO: 17) THTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVD(A)VSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCK(A)VSNKALPVPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGPFFLYSKLTVDKSRWQQGNVFSCSVMHEALHN(A)HYTQKSLSLSPGK.

In some embodiments, the Fc domain can comprise or consist of thefollowing amino acid sequence:

(SEQ ID NO: 21) KSSDKTHTCP PCPAPELLGG PSVFLFPPKP KDTLMISRTPEVTCVVVDVS HEDPEVKFNW YVDGVEVHNA KTKPREEQYNSTYRVVSVLT VLHQDWLNGK EYKCKVSNKA LPAPIEKTISKAKGQPREPQ VYTLPPSRDE LTKNQVSLTC LVKGFYPSDIAVEWESNGQP ENNYKTTPPV LDSDGSFFLY SKLTVDKSRW QQGNVFSCSV MHEALHNHYT QKSLSLSPGK.

In some embodiments, the fusion protein comprises the following aminoacid sequence:

(SEQ ID NO: 10) MTWRHHVRLL FTVSLALQII NLGNSYQREK HNGGREEVTKVATQKHRQSP LNWTSSHFGE VTGSAEGWGP EEPLPYSRAFGEGASARPRC CRNGGTCVLG SFCVCPAHFT GRYCEHDQRRSECGALEHGA WTLRACHLCR CIFGALHCLP LQTPDRCDPKENLYFQGGGSGGSGGDYKDDDD KSSDKTHTCPPCPAPELLGG PSVFLFPPKP KDTLMISRTP EVTCVVVDVSHEDPEVKFNW YVDGVEVHNA KTKPREEQYN STYRVVSVLTVLHQDWLNGK EYKCKVSNKA LPAPIEKTIS KAKGQPREPQVYTLPPSRDE LTKNQVSLTC LVKGFYPSDI AVEWESNGQPENNYKTTPPV LDSDGSFFLY SKLTVDKSRW QQGNVFSCSV MHEALHNHYT QKSLSLSPGK.The linker sequence is in bold, whereas the Fc region of the fusionprotein is underlined. The remaining sequence corresponds to a fragmentof human Cryptic.

In some embodiments, the fusion protein comprises the following aminoacid sequence:

(SEQ ID NO: 22) YQREK HNGGREEVTK VATQKHRQSP LNWTSSHFGE VTGSAEGWGPEEPLPYSRAF GEGASARPRC CRNGGTCVLG SFCVCPAHFTGRYCEHDQRR SECGALEHGA WTLRACHLCR CIFGALHCLPLQTPDRCDPK ENLYFQGGGSGGSGGDYKDDDD KSSDKTHTCPPCPAPELLGG PSVFLFPPKP KDTLMISRTP EVTCVVVDVSHEDPEVKFNW YVDGVEVHNA KTKPREEQYN STYRVVSVLTVLHQDWLNGK EYKCKVSNKA LPAPIEKTIS KAKGQPREPQVYTLPPSRDE LTKNQVSLTC LVKGFYPSDI AVEWESNGQPENNYKTTPPV LDSDGSFFLY SKLTVDKSRW QQGNVFSCSV MHEALHNHYT QKSLSLSPGK.The linker sequence is in bold, whereas the Fc region of the fusionprotein is underlined. The remaining sequence is a fragment of humanCryptic.

It may be useful, in some circumstances, to modify the immunoglobulinheavy chain constant region, for example, by mutation, deletion or otherchanges mediated by genetic engineering or other approaches, so thatcertain activities, such as complement fixation or stimulation ofantibody-dependent cell-mediated cytotoxicity (ADCC) are reduced oreliminated, while preferably preserving the Fc regions' ability to bindan Fc receptor (e.g., FcRn).

In some embodiments, the Fc region (including those of an antibody orantigen-binding fragment described herein) can be an altered Fc constantregion having reduced (or no) effector function relative to itscorresponding unaltered constant region. Effector functions involvingthe Fc constant region may be modulated by altering properties of theconstant or Fc region. Altered effector functions include, for example,a modulation in one or more of the following activities:antibody-dependent cellular cytotoxicity (ADCC), complement-dependentcytotoxicity (CDC), apoptosis, binding to one or more Fc-receptors, andpro-inflammatory responses. Modulation refers to an increase, decrease,or elimination of an effector function activity exhibited by a subjectantibody containing an altered constant region as compared to theactivity of the unaltered form of the constant region. In particularembodiments, modulation includes situations in which an activity isabolished or completely absent. For example, an altered Fc constantregion that displays modulated ADCC and/or CDC activity may exhibitapproximately 0 to 50% (e.g., less than 50, 49, 48, 47, 46, 45, 44, 43,42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25,24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6,5, 4, 3, 2, or 1%) of the ADCC and/or CDC activity of the unaltered formof the Fc constant region. An altered Fc region described herein mayexhibit reduced or no measurable ADCC and/or CDC activity.

In certain embodiments, the altered constant region has at least oneamino acid substitution, insertion, and/or deletion, compared to anative sequence constant region or to the unaltered constant region,e.g. from about one to about one hundred amino acid substitutions,insertions, and/or deletions in a native sequence constant region or inthe constant region of the parent polypeptide. In some embodiments, thealtered constant region herein will possess at least about 70% homology(similarity) or identity with the unaltered constant region and in someinstances at least about 75% and in other instances at least about 80%homology or identity therewith, and in other embodiments at least about85%, 90% or 95% homology or identity therewith. The altered constantregion may also contain one or more amino acid deletions or insertions.Additionally, the altered constant region may contain one or more aminoacid substitutions, deletions, or insertions that results in alteredpost-translational modifications, including, for example, an alteredglycosylation pattern (e.g., the addition of one or more sugarcomponents, the loss of one or more sugar components, or a change incomposition of one or more sugar components relative to the unalteredconstant region).

Altered Fc constant regions may be generated by engineering or producingantibodies with variant constant, Fc, or heavy chain regions;recombinant DNA technology and/or cell culture and expression conditionsmay be used to produce antibodies with altered function and/or activity.For example, recombinant DNA technology may be used to engineer one ormore amino acid substitutions, deletions, or insertions in regions (suchas, for example, Fc or constant regions) that affect antibody functionincluding effector functions. Alternatively, changes inpost-translational modifications, such as, e.g., glycosylation patterns,may be achieved by manipulating the cell culture and expressionconditions by which the antibody is produced. Suitable methods forintroducing one or more substitutions, additions, or deletions into anFc region of an antibody are well known in the art and include, e.g.,standard DNA mutagenesis techniques as described in, e.g., Sambrook etal. (1989) “Molecular Cloning: A Laboratory Manual, 2^(nd) Edition,”Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; PCTpublication no. WO 06/53301; and U.S. Pat. No. 7,704,497, thedisclosures of each of which are incorporated herein by reference intheir entirety.

Altered Fc constant regions having reduced effector function may beproduced by introducing other types of changes in the amino acidsequence of certain regions of the antibody. Such amino acid sequencechanges include but are not limited to the Ala-Ala mutation describedin, e.g., PCT Publication nos. WO 94/28027 and WO 98/47531; and Xu etal. (2000) Cell Immunol 200:16-26. According to these embodiments, theFc constant region comprises a substitution to an alanine at position234 or a mutation to an alanine at position 235. Additionally, thealtered constant region may contain a double mutation: a mutation to analanine at position 234 and a second mutation to an alanine at position235. In one embodiment, the Fc constant region comprises an IgG4framework, wherein the Ala-Ala mutation would describe a mutation(s)from phenylalanine to alanine at position 234 and/or a mutation fromleucine to alanine at position 235. In another embodiment, the Fcconstant region comprises an IgG1 framework, wherein the Ala-Alamutation would describe a mutation(s) from leucine to alanine atposition 234 and/or a mutation from leucine to alanine at position 235.An Fc constant region may alternatively or additionally carry othermutations, including the point mutation K322A in the CH2 domain (Hezarehet al. (2001) J Virol 75:12161-12168).

Additional substitutions that, when introduced into a heavy chainconstant region, result in decreased effector function are set forth in,e.g., Shields et al. (2001) J Biol Chem 276(9):6591-6604. Seeparticularly Table 1 (“Binding of human IgG1 variants to human FcRn andFcγR) of Shields et al., the disclosure of which is incorporated hereinby reference in its entirety. By screening a library of anti-IgEantibodies, each antibody of the library differing by one or moresubstitutions in the heavy chain constant region, for binding to a panelof Fc receptors (including FcRn, FcγRI, FcγRIIA, FcγRIIB, and FcγRIIIA),the authors identified a number of substitutions that modulate specificFc-Fc receptor interactions. For example, a variant IgG2a heavy chainconstant region in which the CH2 domain contains a D265A substitution(heavy chain amino acid numbering according to Kabat et al. (supra))results in a complete loss of interaction between the variant constantregion and IgG Fc receptors FcγRIIB, FcγRIII, FcγRI, and FcγRIV. Shieldset al. (2001) at page 6595, Table 1. See also Baudino et al. (2008) JImmunol 181:6664-6669 (supra).

Changes within the hinge region also affect effector functions. Forexample, deletion of the hinge region may reduce affinity for Fcreceptors and may reduce complement activation (Klein et al. (1981) ProcNatl Acad Sci USA 78: 524-528). The present disclosure therefore alsorelates to antibodies with alterations in the hinge region.

In some embodiments, an altered Fc constant region (e.g., an alteredhuman Fc constant region) can bind to neonatal Fc receptor (FcRn) withgreater affinity than that of the native Fc constant region from whichthe altered or variant Fc constant region was derived. For example, theFc constant region can comprise one or more (e.g., two, three, four,five, six, seven, or eight or more) amino acid substitutions relative tothe native human Fc constant region from which the variant human Fcconstant region was derived. The substitutions can increase the bindingaffinity of an IgG antibody containing the variant Fc constant region toFcRn at pH 6.0, while maintaining the pH dependence of the interaction.See, e.g., Hinton et al. (2004) J Biol Chem 279:6213-6216 andDatta-Mannan et al. (2007) Drug Metab Dispos 35:1-9. Methods for testingwhether one or more substitutions in the Fc constant region of anantibody increase the affinity of the Fc constant region for FcRn at pH6.0 (while maintaining pH dependence of the interaction) are known inthe art and exemplified in the working examples. See, e.g., Datta-Mannanet al. (2007) J Biol Chem 282(3):1709-1717; International PublicationNo. WO 98/23289; International Publication No. WO 97/34631; and U.S.Pat. No. 6,277,375, the disclosures of each of which are incorporatedherein by reference in their entirety.

Substitutions that enhance the binding affinity of an antibody Fcconstant region for FcRn are known in the art and include, e.g., (1) theM252Y/S254T/TT256E triple substitution described by Dall'Acqua et al.(2006) J Biol Chem 281: 23514-23524; (2) the M428L or T250Q/M428Lsubstitutions described in Hinton et al. (2004) J Biol Chem279:6213-6216 and Hinton et al. (2006) J Immunol 176:346-356; and (3)the N434A or T307/E380A/N434A substitutions described in Petkova et al.(2006) Int Immunol 18(12):1759-69. The additional substitution pairings:P257I/Q311I, P257I/N434H, and D376V/N434H are described in, e.g.,Datta-Mannan et al. (2007) J Biol Chem 282(3):1709-1717, the disclosureof which is incorporated herein by reference in its entirety.

In some embodiments, the variant constant region has a substitution atEU amino acid residue 255 for valine. In some embodiments, the variantconstant region has a substitution at EU amino acid residue 309 forasparagine. In some embodiments, the variant constant region has asubstitution at EU amino acid residue 312 for isoleucine. In someembodiments, the variant constant region has a substitution at EU aminoacid residue 386.

In some embodiments, the variant Fc constant region comprises no morethan 30 (e.g., no more than 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19,18, 17, 16, 15, 14, 13, 12, 11, 10, nine, eight, seven, six, five, four,three, or two) amino acid substitutions, insertions, or deletionsrelative to the native constant region from which it was derived. Insome embodiments, the variant Fc constant region comprises one or moreamino acid substitutions selected from the group consisting of: M252Y,S254T, T256E, N434S, M428L, V259I, T250I, and V308F. In someembodiments, the variant human Fc constant region comprises a methionineat position 428 and an asparagine at position 434, each in EU numbering.In some embodiments, the variant Fc constant region comprises a428L/434S double substitution as described in, e.g., U.S. Pat. No.8,088,376.

In some embodiments, the altered or variant Fc constant region comprisesa substitution at amino acid position 237, 238, 239, 248, 250, 252, 254,255, 256, 257, 258, 265, 270, 286, 289, 297, 298, 303, 305, 307, 308,309, 311, 312, 314, 315, 317, 325, 332, 334, 360, 376, 380, 382, 384,385, 386, 387, 389, 424, 428, 433, 434, or 436 (EU numbering) relativeto the native human Fc constant region. In some embodiments, thesubstitution is selected from the group consisting of: methionine forglycine at position 237; alanine for proline at position 238; lysine forserine at position 239; isoleucine for lysine at position 248; alanine,phenylalanine, isoleucine, methionine, glutamine, serine, valine,tryptophan, or tyrosine for threonine at position 250; phenylalanine,tryptophan, or tyrosine for methionine at position 252; threonine forserine at position 254; glutamic acid for arginine at position 255;aspartic acid, glutamic acid, or glutamine for threonine at position256; alanine, glycine, isoleucine, leucine, methionine, asparagine,serine, threonine, or valine for proline at position 257; histidine forglutamic acid at position 258; alanine for aspartic acid at position265; phenylalanine for aspartic acid at position 270; alanine, orglutamic acid for asparagine at position 286; histidine for threonine atposition 289; alanine for asparagine at position 297; glycine for serineat position 298; alanine for valine at position 303; alanine for valineat position 305; alanine, aspartic acid, phenylalanine, glycine,histidine, isoleucine, lysine, leucine, methionine, asparagine, proline,glutamine, arginine, serine, valine, tryptophan, or tyrosine forthreonine at position 307; alanine, phenylalanine, isoleucine, leucine,methionine, proline, glutamine, or threonine for valine at position 308;alanine, aspartic acid, glutamic acid, proline, or arginine for leucineor valine at position 309; alanine, histidine, or isoleucine forglutamine at position 311; alanine, or histidine for aspartic acid atposition 312; lysine, or arginine for leucine at position 314; alanine,or histidine for asparagine at position 315; alanine for lysine atposition 317; glycine for asparagine at position 325; valine forisoleucine at position 332; leucine for lysine at position 334;histidine for lysine at position 360; alanine for aspartic acid atposition 376; alanine for glutamic acid at position 380; alanine forglutamic acid at position 382; alanine for asparagine or serine atposition 384; aspartic acid, or histidine for glycine at position 385;proline for glutamine at position 386; glutamic acid for proline atposition 387; alanine, or serine for asparagine at position 389; alaninefor serine at position 424; alanine, aspartic acid, phenylalanine,glycine, histidine, isoleucine, lysine, leucine, asparagine, proline,glutamine, serine, threonine, valine, tryptophan, or tyrosine formethionine at position 428; lysine for histidine at position 433;alanine, phenylalanine, histidine, serine, tryptophan, or tyrosine forasparagine at position 434; and histidine for tyrosine or phenylalanineat position 436, all in EU numbering.

It is understood that different elements of the fusion proteins may bearranged in any manner that is consistent with the desiredfunctionality. For example, a Cryptic polypeptide may be placedC-terminal to a heterologous domain, or, alternatively, a heterologousdomain may be placed C-terminal to a Cryptic polypeptide. The Crypticpolypeptide domain and the heterologous domain need not be adjacent in afusion protein, and additional domains or amino acid sequences may beincluded C- or N-terminal to either domain or between the domains.

Polypeptide Expression

A recombinant polypeptide (e.g., fragments or fusion proteins) can beproduced using a variety of techniques known in the art of molecularbiology and protein chemistry. For example, a nucleic acid encoding afusion protein can be inserted into an expression vector that containstranscriptional and translational regulatory sequences, which include,e.g., promoter sequences, ribosomal binding sites, transcriptional startand stop sequences, translational start and stop sequences,transcription terminator signals, polyadenylation signals, and enhanceror activator sequences. The regulatory sequences include a promoter andtranscriptional start and stop sequences. In addition, the expressionvector can include more than one replication system such that it can bemaintained in two different organisms, for example in mammalian orinsect cells for expression and in a prokaryotic host for cloning andamplification.

Several possible vector systems are available for the expression ofrecombinant polypeptides from nucleic acids in mammalian cells. Oneclass of vectors relies upon the integration of the desired genesequences into the host cell genome. Cells which have stably integratedDNA can be selected by simultaneously introducing drug resistance genessuch as E. coli gpt (Mulligan and Berg (1981) Proc Natl Acad Sci USA78:2072) or Tn5 neo (Southern and Berg (1982) Mol Appl Genet 1:327). Theselectable marker gene can be either linked to the DNA gene sequences tobe expressed, or introduced into the same cell by co-transfection(Wigler et al. (1979) Cell 16:77). A second class of vectors utilizesDNA elements which confer autonomously replicating capabilities to anextrachromosomal plasmid. These vectors can be derived from animalviruses, such as bovine papillomavirus (Sarver et al. (1982) Proc NatlAcad Sci USA, 79:7147), cytomegalovirus, polyoma virus (Deans et al.(1984) Proc Natl Acad Sci USA 81:1292), or SV40 virus (Lusky and Botchan(1981) Nature 293:79).

The expression vectors can be introduced into cells in a manner suitablefor subsequent expression of the nucleic acid. The method ofintroduction is largely dictated by the targeted cell type, discussedbelow. Exemplary methods include CaPO₄ precipitation, liposome fusion,cationic liposomes, electroporation, viral infection, dextran-mediatedtransfection, polybrene-mediated transfection, protoplast fusion, anddirect microinjection.

Appropriate host cells for the expression of recombinant proteinsinclude yeast, bacteria, insect, plant, and mammalian cells (e.g.,rodent cell lines, such as Chinese Hamster Ovary (CHO) cells). Ofparticular interest are bacteria such as E. coli, fungi such asSaccharomyces cerevisiae and Pichia pastoris, insect cells such as SF9,mammalian cell lines (e.g., human cell lines), as well as primary celllines.

In some embodiments, a recombinant protein can be expressed in, andpurified from, transgenic animals (e.g., transgenic mammals). Forexample, a recombinant protein can be produced in transgenic non-humanmammals (e.g., rodents) and isolated from milk as described in, e.g.,Houdebine (2002) Curr Opin Biotechnol 13(6):625-629; van Kuik-Romeijn etal. (2000) Transgenic Res 9(2):155-159; and Pollock et al. (1999) JImmunol Methods 231(1-2):147-157.

A polypeptide can be produced from the cells by culturing a host celltransformed with the expression vector containing nucleic acid encodingthe polypeptide, under conditions, and for an amount of time, sufficientto allow expression of the proteins. Such conditions for proteinexpression will vary with the choice of the expression vector and thehost cell, and will be easily ascertained by one skilled in the artthrough routine experimentation. For example, proteins expressed in E.coli can be refolded from inclusion bodies (see, e.g., Hou et al. (1998)Cytokine 10:319-30). Bacterial expression systems and methods for theiruse are well known in the art (see Current Protocols in MolecularBiology, Wiley & Sons, and Molecular Cloning—A Laboratory Manual—3rdEd., Cold Spring Harbor Laboratory Press, New York (2001)). The choiceof codons, suitable expression vectors and suitable host cells will varydepending on a number of factors, and may be easily optimized as needed.A fusion protein described herein can be expressed in mammalian cells orin other expression systems including but not limited to yeast,baculovirus, and in vitro expression systems (see, e.g., Kaszubska etal. (2000) Protein Expression and Purification 18:213-220).

Following expression, the recombinant proteins can be isolated. The term“purified” or “isolated” as applied to any of the proteins describedherein refers to a polypeptide that has been separated or purified fromcomponents (e.g., proteins or other naturally-occurring biological ororganic molecules) which naturally accompany it, e.g., other proteins,lipids, and nucleic acid in a prokaryotic or eukaryotic cell expressingthe proteins. Typically, a polypeptide is purified when it constitutesat least 60 (e.g., at least 65, 70, 75, 80, 85, 90, 92, 95, 97, or 99)%, by weight, of the total protein in a sample.

The recombinant proteins can be isolated or purified in a variety ofways known to those skilled in the art depending on what othercomponents are present in the sample. Standard purification methodsinclude electrophoretic, molecular, immunological, and chromatographictechniques, including ion exchange, hydrophobic, affinity, andreverse-phase HPLC chromatography. For example, an antibody can bepurified using a standard anti-antibody column (e.g., a protein-A orprotein-G column). Ultrafiltration and diafiltration techniques, inconjunction with protein concentration, are also useful. See, e.g.,Scopes (1994) “Protein Purification, 3^(rd) edition,” Springer-Verlag,New York City, N.Y. The degree of purification necessary will varydepending on the desired use. In some instances, no purification of theexpressed proteins will be necessary.

Methods for determining the yield or purity of a purified protein areknown in the art and include, e.g., Bradford assay, UV spectroscopy,Biuret protein assay, Lowry protein assay, amido black protein assay,high pressure liquid chromatography (HPLC), mass spectrometry (MS), andgel electrophoretic methods (e.g., using a protein stain such asCoomassie Blue or colloidal silver stain).

In some embodiments, endotoxin can be removed from the proteinpreparations. Methods for removing endotoxin from a protein sample areknown in the art and exemplified in the working examples. For example,endotoxin can be removed from a protein sample using a variety ofcommercially available reagents including, without limitation, theProteoSpin™ Endotoxin Removal Kits (Norgen Biotek Corporation),Detoxi-Gel Endotoxin Removal Gel (Thermo Scientific; Pierce ProteinResearch Products), MiraCLEAN® Endotoxin Removal Kit (Mirus), orAcrodisc™—Mustang® E membrane (Pall Corporation).

Methods for detecting and/or measuring the amount of endotoxin presentin a sample (both before and after purification) are known in the artand commercial kits are available. For example, the concentration ofendotoxin in a protein sample can be determined using the QCL-1000Chromogenic kit (BioWhittaker), the limulus amebocyte lysate (LAL)-basedkits such as the Pyrotell®, Pyrotell®-T, Pyrochrome®, Chromo-LAL, andCSE kits available from the Associates of Cape Cod Incorporated.

Pharmaceutical Compositions and Formulations

The compositions described herein can be formulated as a pharmaceuticalsolution, e.g., for administration to a subject for enhancing an immuneresponse to an antigen. The pharmaceutical compositions will generallyinclude a pharmaceutically acceptable carrier. As used herein, a“pharmaceutically acceptable carrier” refers to, and includes, any andall solvents, dispersion media, coatings, antibacterial and antifungalagents, isotonic and absorption delaying agents, and the like that arephysiologically compatible. The compositions can include apharmaceutically acceptable salt, e.g., an acid addition salt or a baseaddition salt (see e.g., Berge et al. (1977) J Pharm Sci 66:1-19).

The compositions can be formulated according to standard methods.Pharmaceutical formulation is a well-established art, and is furtherdescribed in, e.g., Gennaro (2000) “Remington: The Science and Practiceof Pharmacy,” 20^(th) Edition, Lippincott, Williams & Wilkins (ISBN:0683306472); Ansel et al. (1999) “Pharmaceutical Dosage Forms and DrugDelivery Systems,” 7^(th) Edition, Lippincott Williams & WilkinsPublishers (ISBN: 0683305727); and Kibbe (2000) “Handbook ofPharmaceutical Excipients American Pharmaceutical Association,” 3^(rd)Edition (ISBN: 091733096X). In some embodiments, a composition can beformulated, for example, as a buffered solution at a suitableconcentration and suitable for storage at 2-8° C. (e.g., 4° C.). In someembodiments, a composition can be formulated for storage at atemperature below 0° C. (e.g., −20° C. or −80° C.). In some embodiments,the composition can be formulated for storage for up to 2 years (e.g.,one month, two months, three months, four months, five months, sixmonths, seven months, eight months, nine months, 10 months, 11 months, 1year, 1½ years, or 2 years) at 2-8° C. (e.g., 4° C.). Thus, in someembodiments, the compositions described herein are stable in storage forat least 1 year at 2-8° C. (e.g., 4° C.).

The pharmaceutical compositions can be in a variety of forms. Theseforms include, e.g., liquid, semi-solid and solid dosage forms, such asliquid solutions (e.g., injectable and infusible solutions), dispersionsor suspensions, tablets, pills, powders, liposomes and suppositories.The preferred form depends, in part, on the intended mode ofadministration and therapeutic application. For example, compositionscontaining a composition intended for systemic or local delivery can bein the form of injectable or infusible solutions. Accordingly, thecompositions can be formulated for administration by a parenteral mode(e.g., intravenous, subcutaneous, intraperitoneal, or intramuscularinjection). “Parenteral administration,” “administered parenterally,”and other grammatically equivalent phrases, as used herein, refer tomodes of administration other than enteral and topical administration,usually by injection, and include, without limitation, intravenous,intranasal, intraocular, pulmonary, intramuscular, intraarterial,intrathecal, intracapsular, intraorbital, intracardiac, intradermal,intrapulmonary, intraperitoneal, transtracheal, subcutaneous,subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal,epidural, intracerebral, intracranial, intracarotid and intrasternalinjection and infusion (see below).

The compositions can be formulated as a solution, microemulsion,dispersion, liposome, or other ordered structure suitable for stablestorage at high concentration. Sterile injectable solutions can beprepared by incorporating a composition described herein in the requiredamount in an appropriate solvent with one or a combination ofingredients enumerated above, as required, followed by filteredsterilization. Generally, dispersions are prepared by incorporating acomposition described herein into a sterile vehicle that contains abasic dispersion medium and the required other ingredients from thoseenumerated above. In the case of sterile powders for the preparation ofsterile injectable solutions, methods for preparation include vacuumdrying and freeze-drying that yield a powder of a composition describedherein plus any additional desired ingredient (see below) from apreviously sterile-filtered solution thereof. The proper fluidity of asolution can be maintained, for example, by the use of a coating such aslecithin, by the maintenance of the required particle size in the caseof dispersion and by the use of surfactants. Prolonged absorption ofinjectable compositions can be brought about by including in thecomposition a reagent that delays absorption, for example, monostearatesalts, and gelatin.

The compositions described herein can also be formulated inimmunoliposome compositions. Such formulations can be prepared bymethods known in the art such as, e.g., the methods described in Epsteinet al. (1985) Proc Natl Acad Sci USA 82:3688; Hwang et al. (1980) ProcNatl Acad Sci USA 77:4030; and U.S. Pat. Nos. 4,485,045 and 4,544,545.Liposomes with enhanced circulation time are disclosed in, e.g., U.S.Pat. No. 5,013,556.

In certain embodiments, compositions can be formulated with a carrierthat will protect the compound against rapid release, such as acontrolled release formulation, including implants and microencapsulateddelivery systems. Biodegradable, biocompatible polymers can be used,such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid,collagen, polyorthoesters, and polylactic acid. Many methods for thepreparation of such formulations are known in the art. See, e.g., J. R.Robinson (1978) “Sustained and Controlled Release Drug DeliverySystems,” Marcel Dekker, Inc., New York.

In some embodiments, compositions described herein are administered inan aqueous solution by parenteral injection. The disclosure featurespharmaceutical compositions comprising an effective amount of the agent(or more than one agent) and optionally include pharmaceuticallyacceptable diluents, preservatives, solubilizers, emulsifiers, adjuvantsand/or carriers. Such compositions include sterile water, bufferedsaline (e.g., Tris-HCl, acetate, phosphate), pH and ionic strength; andoptionally, additives such as detergents and solubilizing agents (e.g.,TWEEN® 20, TWEEN 80, Polysorbate 80), anti-oxidants (e.g., ascorbicacid, sodium metabisulfite), and preservatives (e.g., thimersol, benzylalcohol) and bulking substances (e.g., lactose, mannitol). Theformulations may be sterilized, e.g., using filtration, incorporatingsterilizing agents into the compositions, by irradiating thecompositions, or by heating the compositions.

As described above, relatively high concentration compositions can bemade. For example, the compositions can be formulated at a concentrationof between about 10 mg/mL to 100 mg/mL (e.g., between about 9 mg/mL and90 mg/mL; between about 9 mg/mL and 50 mg/mL; between about 10 mg/mL and50 mg/mL; between about 15 mg/mL and 50 mg/mL; between about 15 mg/mLand 110 mg/mL; between about 15 mg/mL and 100 mg/mL; between about 20mg/mL and 100 mg/mL; between about 20 mg/mL and 80 mg/mL; between about25 mg/mL and 100 mg/mL; between about 25 mg/mL and 85 mg/mL; betweenabout 20 mg/mL and 50 mg/mL; between about 25 mg/mL and 50 mg/mL;between about 30 mg/mL and 100 mg/mL; between about 30 mg/mL and 50mg/mL; between about 40 mg/mL and 100 mg/mL; between about 50 mg/mL and100 mg/mL; or between about 20 mg/mL and 50 mg/mL). In some embodiments,compositions can be formulated at a concentration of greater than 5mg/mL and less than 50 mg/mL. Methods for formulating a protein in anaqueous solution are known in the art and are described in, e.g., U.S.Pat. No. 7,390,786; McNally and Hastedt (2007), “Protein Formulation andDelivery,” Second Edition, Drugs and the Pharmaceutical Sciences, Volume175, CRC Press; and Banga (1995), “Therapeutic peptides and proteins:formulation, processing, and delivery systems,” CRC Press. In someembodiments, the aqueous solution has a neutral pH, e.g., a pH between,e.g., 6.5 and 8 (e.g., between and inclusive of 7 and 8). In someembodiments, the aqueous solution has a pH of about 6.6, 6.7, 6.8, 6.9,7, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0. In someembodiments, the aqueous solution has a pH of greater than (or equal to)6 (e.g., greater than or equal to 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7,6.8, 6.9, 7, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, or 7.9), but lessthan pH 8.

As used herein, “about” and like grammatical terms refers to anacceptable degree of error for the quantity measured given the nature orprecision of the measurements. Exemplary degrees of error include up to20% (e.g., no more than 19, 18, 17, 16, 15, 14, 12, 11, 10, 9, 8, 7, 6,5, 4, 3, 2, 1, or less than 1%). In some embodiments, e.g., inbiological systems, about includes values that are within an order ofmagnitude, e.g., within 4-fold, 3-fold, or 2-fold. In some embodiments,“about” refers to a value no more than 100% of the stated referencevalue.

Nucleic acids encoding a therapeutic polypeptide can be incorporatedinto a gene construct to be used as a part of a gene therapy protocol todeliver nucleic acids that can be used to express and produce agentswithin cells. Expression constructs of such components may beadministered in any therapeutically effective carrier, e.g. anyformulation or composition capable of effectively delivering thecomponent gene to cells in vivo. Approaches include insertion of thesubject gene in viral vectors including recombinant retroviruses,adenovirus, adeno-associated virus, lentivirus, and herpes simplexvirus-1 (HSV-1), or recombinant bacterial or eukaryotic plasmids. Viralvectors can transfect cells directly; plasmid DNA can be delivered withthe help of, for example, cationic liposomes (lipofectin) orderivatized, polylysine conjugates, gramicidin S, artificial viralenvelopes or other such intracellular carriers, as well as directinjection of the gene construct or CaPO₄ precipitation (see, e.g.,WO04/060407) carried out in vivo. Examples of suitable retrovirusesinclude pLJ, pZIP, pWE and pEM which are known to those skilled in theart (see, e.g., Eglitis et al. (1985) Science 230:1395-1398; Danos andMulligan (1988) Proc Natl Acad Sci USA 85:6460-6464; Wilson et al.(1988) Proc Natl Acad Sci USA 85:3014-3018; Armentano et al. (1990)Proc. Natl. Acad. Sci. USA 87:6141-6145; Huber et al. (1991) Proc NatlAcad Sci USA 88:8039-8043; Ferry et al. (1991) Proc Natl Acad Sci USA88:8377-8381; Chowdhury et al. (1991) Science 254:1802-1805; vanBeusechem et al. (1992) Proc Natl Acad Sci USA 89:7640-7644; Kay et al.(1992) Human Gene Therapy 3:641-647; Dai et al. (1992) Proc Natl AcadSci USA 89:10892-10895; Hwu et al. (1993) J Immunol 150:4104-4115; U.S.Pat. Nos. 4,868,116 and 4,980,286; PCT Publication Nos. WO89/07136,WO89/02468, WO89/05345, and WO92/07573). Another viral gene deliverysystem utilizes adenovirus-derived vectors (see, e.g., Berkner et al.(1988) BioTechniques 6:616; Rosenfeld et al. (1991) Science 252:431-434;and Rosenfeld et al. (1992) Cell 68:143-155). Suitable adenoviralvectors derived from the adenovirus strain Ad type 5 d1324 or otherstrains of adenovirus (e.g., Ad2, Ad3, Ad7, etc.) are known to thoseskilled in the art. Yet another viral vector system useful for deliveryof the subject gene is the adeno-associated virus (AAV). See, e.g.,Flotte et al. (1992) Am J Respir Cell Mot Biol 7:349-356; Samulski etal. (1989) J Virol 63:3822-3828; and McLaughlin et al. (1989)J Virol62:1963-1973.

In some embodiments, compositions can be formulated with one or moreadditional therapeutic agents, e.g., additional agents for increasingbone formation, bone density, or bone mass.

When compositions are to be used in combination with a second activeagent, the compositions can be coformulated with the second agent or thecompositions can be formulated separately from the second agentformulation. For example, the respective pharmaceutical compositions canbe mixed, e.g., just prior to administration, and administered togetheror can be administered separately, e.g., at the same or different times(see below).

Kits

The disclosure also pertains to packaged pharmaceutical compositions orkits for administering any one or more of the polypeptides describedherein, e.g., for the treatment of a condition associated with bone lossor any other condition described herein (e.g., a cancer, a metabolicdisorder, a muscle wasting disorder, a musculoskeletal disorder, or animmune disorder). In some embodiments, the kit comprises one or more ofthe polypeptides described herein and instructions for administration ofpolypeptide(s) for treatment of the condition. The instructions maydescribe how, e.g., subcutaneously or intravenously, and when, e.g., atweek 0, week 2, week 4, etc., the different doses of the one or morepolypeptides shall be administered to a subject for treatment.

Another aspect of the invention pertains to kits containing apharmaceutical composition comprising one or more of the polypeptidesdescribed herein and a pharmaceutically acceptable carrier, and one ormore pharmaceutical compositions each comprising an additionaltherapeutic agent useful for treating a condition associated with boneloss, and a pharmaceutically acceptable carrier. Alternatively, the kitcomprises a single pharmaceutical composition comprising one or more ofthe polypeptides described herein, one or more drugs useful for treatinga subject in need thereof (e.g., a subject having a condition associatedwith bone loss), and a pharmaceutically acceptable carrier. Theinstructions may describe how, e.g., subcutaneously, and when, e.g., atweek 0, week 2, week 4, etc., the different doses of the one or morepolypeptides and/or the additional therapeutic agent shall beadministered to a subject for treatment. The kit may containinstructions for dosing of the pharmaceutical compositions for thetreatment of a condition described herein, e.g., a condition associatedwith bone loss.

In some embodiments, the kit comprises one or more reagents and/orinstructions for testing for an improvement in at least one indicia ofbone growth, bone density, bone strength, bone formation, etc.

Therapeutic Applications

The polypeptides described herein can be used in a number of therapeuticapplications. For example, the polypeptides can increase bone formation,bone mass, bone density, bone strength, and the like. As such, thepolypeptides are useful in a variety of therapeutic applications, e.g.,for treating or preventing a disease or condition associated with boneloss, insufficiency, or damage. For example, the Cryptic polypeptidesdescribed herein are useful for treating subjects suffering from acondition associated with bone loss, such as osteoporosis or Paget'sdisease. In some embodiments, the disclosure provides methods oftreating or preventing bone damage in an individual in need thereofthrough administering to the individual a therapeutically effectiveamount of a polypeptide described herein. In some embodiments, thedisclosure provides methods of promoting bone growth or mineralizationin an individual in need thereof through administering to the individuala therapeutically effective amount of a polypeptide described herein.These methods are preferably aimed at therapeutic and prophylactictreatments of animals, and more preferably, humans. In some embodiments,the disclosure provides for the use of a polypeptide described hereinfor the treatment of disorders associated with low bone density ordecreased bone strength.

The compositions described herein can be administered to a subject,e.g., a human subject, using a variety of methods that depend, in part,on the route of administration. The route can be, e.g., intravenousinjection or infusion (IV), subcutaneous injection (SC), intraperitoneal(IP) injection, or intramuscular injection (IM).

Administration can be achieved by, e.g., local infusion, injection, orby means of an implant. The implant can be of a porous, non-porous, orgelatinous material, including membranes, such as sialastic membranes,or fibers. The implant can be configured for sustained or periodicrelease of the composition to the subject. See, e.g., U.S. PatentApplication Publication No. 20080241223; U.S. Pat. Nos. 5,501,856;4,863,457; and 3,710,795; EP488401; and EP 430539, the disclosures ofeach of which are incorporated herein by reference in their entirety.The composition can be delivered to the subject by way of an implantabledevice based on, e.g., diffusive, erodible, or convective systems, e.g.,osmotic pumps, biodegradable implants, electrodiffusion systems,electroosmosis systems, vapor pressure pumps, electrolytic pumps,effervescent pumps, piezoelectric pumps, erosion-based systems, orelectromechanical systems.

As used herein the term “effective amount” or “therapeutically effectiveamount”, in an in vivo setting, means a dosage sufficient to treat,inhibit, or alleviate one or more symptoms of the disorder being treatedor to otherwise provide a desired pharmacologic and/or physiologiceffect (e.g., treat a condition associated with bone loss). The precisedosage will vary according to a variety of factors such assubject-dependent variables (e.g., age, immune system health, etc.), thedisease, and the treatment being effected. Therapeutically effectiveamounts of the agents disclosed herein treat, ameliorate one or moresymptoms, or prevent (e.g., delay the onset or reduce the severity ofonset of symptoms) a condition described herein, such as conditionassociated with bone loss.

Suitable human doses of any of the antibodies or fragments thereofdescribed herein can further be evaluated in, e.g., Phase I doseescalation studies. See, e.g., van Gurp et al. (2008)Am JTransplantation 8(8):1711-1718; Hanouska et al. (2007) Clin Cancer Res13(2, part 1):523-531; and Hetherington et al. (2006) AntimicrobialAgents and Chemotherapy 50(10): 3499-3500.

Toxicity and therapeutic efficacy of such compositions can be determinedby known pharmaceutical procedures in cell cultures or experimentalanimals (e.g., animal models of bone disorders). These procedures can beused, e.g., for determining the LD50 (the dose lethal to 50% of thepopulation) and the ED50 (the dose therapeutically effective in 50% ofthe population). The dose ratio between toxic and therapeutic effects isthe therapeutic index and it can be expressed as the ratio LD50/ED50.Agents that exhibits a high therapeutic index is preferred. Whilecompositions that exhibit toxic side effects may be used, care should betaken to design a delivery system that targets such compounds to thesite of affected tissue and to minimize potential damage to normal cellsand, thereby, reduce side effects.

The data obtained from the cell culture assays and animal studies can beused in formulating a range of dosage for use in humans. The dosage ofsuch antibodies or antigen-binding fragments thereof lies generallywithin a range of circulating concentrations of the polypeptides thatinclude the ED50 with little or no toxicity. The dosage may vary withinthis range depending upon the dosage form employed and the route ofadministration utilized. A therapeutically effective dose can beestimated initially from cell culture assays. A dose can be formulatedin animal models to achieve a circulating plasma concentration rangethat includes the IC₅₀ (i.e., the concentration of the antibody whichachieves a half-maximal inhibition of symptoms) as determined in cellculture. Such information can be used to more accurately determineuseful doses in humans. Levels in plasma may be measured, for example,by high performance liquid chromatography. In some embodiments, e.g.,where local administration is desired, cell culture or animal modelingcan be used to determine a dose required to achieve a therapeuticallyeffective concentration within the local site.

In some embodiments of any of the methods described herein, an agent canbe administered to a mammal in conjunction with one or more additionaltherapeutic agents (e.g., therapeutic agents for treating bonediseases).

As used herein, a subject is preferably a human, but can also be anon-human primate (e.g., monkey, baboon, or chimpanzee), a horse, a cow,a pig, a sheep, a goat, a dog, a cat, a rabbit, a guinea pig, a gerbil,a hamster, a rat, or a mouse. In some embodiments, the subject is adomesticated animal or a farm animal. In some embodiments, the mammal isan infant (e.g., a human infant).

As used herein, a subject “in need of prevention,” “in need oftreatment,” or “in need thereof,” refers to one, who by the judgment ofan appropriate medical practitioner (e.g., a doctor, a nurse, or a nursepractitioner in the case of humans; a veterinarian in the case ofnon-human mammals), would reasonably benefit from a given treatment(e.g., treatment with one or more of the polypeptides described herein).In some embodiments, that subject is one who is diagnosed as having acondition described herein, such as a condition associated with boneloss.

The term “preventing” is art-recognized, and when used in relation to acondition, is well understood in the art, and includes administration ofa composition which reduces the frequency of, or delays the onset of,symptoms of a medical condition in a subject relative to a subject whichdoes not receive the composition.

Also provided herein are methods for inducing bone and/or cartilageformation, preventing bone loss, increasing bone mineralization orpreventing the demineralization of bone. For example, the polypeptidesdescribed herein can be used to treat osteoporosis and to mend bonefractures and cartilage defects in humans and other animals. Thepolypeptides may be useful in patients that are diagnosed withsubclinical low bone density as a protective measure against thedevelopment of osteoporosis.

In some embodiments, one or more of the polypeptides described hereinare useful for healing bone fractures and cartilage defects in humansand other animals. In some embodiments, the polypeptides describedherein can be used in closed as well as open fracture reduction and alsoin the improved fixation of artificial joints. De novo bone formationinduced by an osteogenic agent contributes to the repair of congenital,trauma-induced, or oncologic resection induced craniofacial defects, andalso is useful in cosmetic plastic surgery. In some embodiments, one ormore of the polypeptides can be used to treat osteoporosis.

Conditions associated with bone loss include, without limitation,osteoporosis (including secondary osteoporosis), hyperparathyroidism,Cushing's disease, Paget's disease, thyrotoxicosis, chronic diarrhealstate or malabsorption, renal tubular acidosis, or anorexia nervosa.Osteoporosis may be caused by, or associated with, various factors.Being female, particularly a post-menopausal female, having a low bodyweight, and leading a sedentary lifestyle are all risk factors forosteoporosis (loss of bone mineral density, leading to fracture risk).Persons having any of the following profiles may be candidates fortreatment with one or more of the polypeptides described herein: apost-menopausal woman and not taking estrogen or other hormonereplacement therapy; a person with a personal or maternal history of hipfracture or smoking; a post-menopausal woman who is tall (over 5 feet 7inches) or thin (less than 125 pounds); a man with clinical conditionsassociated with bone loss; a person using medications that are known tocause bone loss, including corticosteroids such as Prednisone™, variousanti-seizure medications such as Dilantin™ and certain barbiturates, orhigh-dose thyroid replacement drugs; a person having type 1 diabetes,liver disease, kidney disease or a family history of osteoporosis; aperson having high bone turnover (e.g., excessive collagen in urinesamples); a person with a thyroid condition, such as hyperthyroidism; aperson who has experienced a fracture after only mild trauma; a personwho has had x-ray evidence of vertebral fracture or other signs ofosteoporosis.

As noted above, osteoporosis can also result as a condition associatedwith another disorder or from the use of certain medications.Osteoporosis resulting from drugs or another medical condition is knownas secondary osteoporosis. In a condition known as Cushing's disease,the excess amount of cortisol produced by the body results inosteoporosis and fractures. The most common medications associated withsecondary osteoporosis are the corticosteroids, a class of drugs thatact like cortisol, a hormone produced naturally by the adrenal glands.Although adequate levels of thyroid hormones (which are produced by thethyroid gland) are needed for the development of the skeleton, excessthyroid hormone can decrease bone mass over time. Antacids that containaluminum can lead to bone loss when taken in high doses by people withkidney problems, particularly those undergoing dialysis. Othermedications that can cause secondary osteoporosis include phenyloin(Dilantin) and barbiturates that are used to prevent seizures;methotrexate (Rheumatrex, Immunex, Folex PFS), a drug for some forms ofarthritis, cancer, and immune disorders; cyclosporine (Sandimmune,Neoral), a drug used to treat some autoimmune diseases and to suppressthe immune system in organ transplant patients; luteinizinghormone-releasing hormone agonists (Lupron, Zoladex), used to treatprostate cancer and endometriosis; heparin (Calciparine, Liquaemin), ananticlotting medication; and cholestyramine (Questran) and colestipol(Colestid), used to treat high cholesterol. Bone loss resulting fromcancer therapy is widely recognized and termed cancer therapy inducedbone loss (CTIBL). Bone metastases can create cavities in the bone thatmay be corrected by treatment with one or more of the polypeptidesdescribed herein. Thus, polypeptides described herein are also usefulfor treating bone loss associated with cancer.

In some embodiments, the polypeptides can be used to increase musclemass or strength in a subject in need thereof. For example, thepolypeptides are useful for treating a subject having a muscle wastingdisorder. In some embodiments, the subject (e.g., a human) to be treatedhas a muscle wasting disorder or suffers from muscle atrophy. A musclewasting disorder, as used herein, encompasses disorders or conditions inwhich muscle wasting is one of the primary symptoms, such as musculardystrophy, spinal cord injury, neurodegenerative diseases, anorexia,sarcopenia, cachexia, muscular atrophy due to immobilization, prolongedbed rest, or weightlessness, and the like, as well as disorders in whichan abnormally high fat-to-muscle ratio is implicated in a disease orpre-disease state, e.g., Type II diabetes or Syndrome X.

Atrophy of skeletal muscle occurs in muscles of adult animals as aresult of lack of use, aging, starvation, and as a consequence of avariety of diseases, disorders, and conditions such as sepsis, musculardystrophy, AIDS, aging, and cancer. The loss of muscle is generallycharacterized by decreases in protein content, force production, fatigueresistance, and muscle fiber diameter. These decreases can be attributedto both a decrease in protein synthesis and an increase in proteindegradation. Muscle wasting and related conditions to which thecompositions and methods of the invention are directed include anycondition in which enhanced muscle growth, or diminishment of musclewasting, produces a therapeutically or otherwise desirable result.Conditions include muscular dystrophy, sarcopenia, cachexia, diabetesmellitus, and the improvement of muscle mass where such improvement isethical and desirable, e.g., in food animals.

One class of muscle wasting disorders, as mentioned above, are themuscular dystrophies. These are a heterogeneous group of neuromusculardisorders, which include the most common type, Duchenne musculardystrophy (DMD), multiple types of limb girdle MD (LGMD) and othercongenital MDs (CMD). Progressive muscle damage and muscle loss, tissueinflammation and replacement of healthy muscle with fibrous and fattytissues result in muscle wasting in muscular dystrophy. Extreme muscleloss is one of the most prominent signs of the disease, and leads tocomplications and symptoms, including death.

Sarcopenia is the age-related loss of muscle mass, strength andfunction. It begins in the fourth decade of life and accelerates afterthe age of approximately 75 years. Many factors, including physicalinactivity, motor-unit remodeling, decreased hormone levels, anddecreased protein synthesis, may all contribute to sarcopenia. With theexception of physical inactivity, all of these may be subject to geneticcontrol where gene modulation may be useful. For example, the rate ofmuscle protein synthesis and protein breakdown affects sarcopenia. Thebalance of protein synthesis and breakdown determines the proteincontent in the body. Research has consistently reported that muscleprotein synthesis rates are lower in older adults when compared toyounger adults. A decrease in muscle protein catabolism, effected by,e.g., gene modulation, could result in slowing or reversal of the lossof muscle mass.

Cachexia is a condition associated with a variety of serious diseases,including cancer, AIDS, septicemia and congestive heart failure. Itsmajor effect is massive loss of both adipose tissue and skeletal muscle,which is not caused by malnutrition. Cachexia contributes to nearlyone-third-of all cancer deaths. In a process that is not yet wellunderstood, cytokines and tumor factors mediate wasting by suppressingmuscle gene products. Cachectic factors have been shown to be selectivein targeting the myosin heavy chain. Cachexia involves a complexdisruption of several systems that also leads to anemia, insulinresistance, immunosuppression, and activation of an acute-phaseresponse. The resulting progressive weakness can make patients withcancer more susceptible to the toxic effects of radiation andchemotherapy; many such patients die from cachexia-related syndromes,rather than from their tumors.

As noted above, the polypeptides described herein bind to and inhibitthe activity of Activin A and Activin B. Activins has been shown toregulate insulin production by pancreatic islets. Tsuchida et al. (2004)Mol Cell Endocrinol 220(1-20):59-65 and Wu et al. (2014) Diabetologia57(1):148-156. Thus, while the disclosure is not bound by any particulartheory or mechanism of action, the polypeptides described herein canalso be useful for treating a metabolic disorder, such as a disorderassociated with insufficient insulin production. The metabolic disordercan be, e.g., type 2 diabetes, noninsulin-dependent diabetes mellitus,hyperglycemia, and obesity.

In another aspect, the disclosure features a method for treating asubject having an immune disorder (e.g., an inflammatory disease orautoimmune disorder). The method comprises administering to the subjectone or more of any of the polypeptides described herein in an amountsufficient to treat the immune disorder. In some embodiments, the immunedisorder is one associated with aberrant host defense response. In someembodiments, the immune disorder can be, e.g.: (a) acute injury oftissues inflicted by infection, toxic substances or trauma, woundhealing pursuant to surgery, severe burns or other tissue injury,meningitis, appendicitis, renal tubular necrosis, traumatic brain injuryand sepsis; (b) autoimmune diseases including, but not limited to,rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease,vasculitis, anti-phospholipid syndrome, scleroderma, systemic lupuserythematosous and osteoarthritis; and (c) respiratory diseasesincluding, but not limited to pneumonia, sarcoidosis, bronchiolitisobliterans, pulmonary hypertension, pneumonia, acute respiratorydistress syndrome, chronic obstructive pulmonary disease (COPD), acuteresponses against infectious agents such as pathogenic virusesincluding, but not limited to, influenza A viruses H5N1 and H1N1,coronaviruses SARS, and human rhinoviruses C and D. See, e.g., Europeanpatent application publication no. 2594280.

The polypeptides are also useful for treating a subject afflicted with aproliferative disorder, such as a cancer. In some embodiments, themammal is one who has, is suspected of having, or is at risk fordeveloping a cancer or an infection. Cancer is a class of diseases ordisorders characterized by uncontrolled division of cells and theability of these to spread, either by direct growth into adjacent tissuethrough invasion, or by implantation into distant sites by metastasis(where cancer cells are transported through the bloodstream or lymphaticsystem). Cancer can affect people at all ages, but risk tends toincrease with age. Types of cancers can include, e.g., lung cancer,breast cancer, colon cancer, pancreatic cancer, renal cancer, stomachcancer, liver cancer, bone cancer, hematological cancer, neural tissuecancer (e.g., neuroblastoma), melanoma, thyroid cancer, ovarian cancer,testicular cancer, prostate cancer, cervical cancer, vaginal cancer, orbladder cancer. Hematological cancers (liquid tumors) include, e.g.,leukemias (e.g., chronic lymphocytic leukemia such as B cell or T celltype chronic lymphocytic leukemia) and multiple myeloma. Bone cancersinclude, without limitation, osteosarcoma and osteocarcinomas.

In some embodiments, the cancer comprises cancer cells that express oneor more receptors for Activin A and/or Activin B. In some embodiments,the cancer comprises cancer cells whose proliferation (e.g., rate ormagnitude of proliferation) and/or viability is positively affected byActivin A or Activin B. See, e.g., Togashi et al. (2015) Cancer Lett356(2 Pt B):819-827; Marino et al. (2014) Mol Hum Reprod20(12):1223-1237; Kang et al. (2009) J Bone Miner Res 24(7):1180-1193;Hoda et al. (2012) Br J Cancer 107:1978-1986; and Wildi et al. (2001)Gut 49(3):409-417. Methods for detecting the presence or expressionlevel of activin receptors by cancer cells are known in the art anddescribed in, e.g., Wildi et al., supra.

Gene expression can be detected as, e.g., protein or mRNA expression ofa protein of interest. That is, the presence or expression level(amount) of a protein can be determined by detecting and/or measuringthe level of mRNA or protein expression.

A variety of suitable methods can be employed to detect and/or measurethe level of mRNA expression of a protein. For example, mRNA expressioncan be determined using Northern blot or dot blot analysis, reversetranscriptase-PCR (RT-PCR; e.g., quantitative RT-PCR), in situhybridization (e.g., quantitative in situ hybridization) or nucleic acidarray (e.g., oligonucleotide arrays or gene chips) analysis. Details ofsuch methods are described below and in, e.g., Sambrook et al.,Molecular Cloning: A Laboratory Manual Second Edition vol. 1, 2 and 3.Cold Spring Harbor Laboratory Press: Cold Spring Harbor, N.Y., USA,November 1989; Gibson et al. (1999) Genome Res 6(10):995-1001; and Zhanget al. (2005) Environ Sci Technol 39(8):2777-2785; U.S. PatentApplication Publication No. 2004086915; European Patent No. 0543942; andU.S. Pat. No. 7,101,663; the disclosures of each of which areincorporated herein by reference in their entirety.

In one example, the presence or amount of one or more discrete mRNApopulations in a biological sample can be determined by isolating totalmRNA from the biological sample (see, e.g., Sambrook et al. (supra) andU.S. Pat. No. 6,812,341) and subjecting the isolated mRNA to agarose gelelectrophoresis to separate the mRNA by size. The size-separated mRNAsare then transferred (e.g., by diffusion) to a solid support such as anitrocellulose membrane. The presence or amount of one or more mRNApopulations in the biological sample can then be determined using one ormore detectably-labeled polynucleotide probes, complementary to the mRNAsequence of interest, which bind to and thus render detectable theircorresponding mRNA populations. Detectable labels include, e.g.,fluorescent (e.g., fluorescein, fluorescein isothiocyanate, rhodamine,dichlorotriazinylamine fluorescein, dansyl chloride, allophycocyanin(APC), or phycoerythrin), luminescent (e.g., europium, terbium, Qdot™nanoparticles supplied by the Quantum Dot Corporation, Palo Alto,Calif.), radiological (e.g., 125I, 131I, 35S, 32P, 33P, or 3H), andenzymatic (horseradish peroxidase, alkaline phosphatase,beta-galactosidase, or acetylcholinesterase) labels.

In another example, the presence or amount of discrete populations ofmRNA in a biological sample can be determined using nucleic acid (oroligonucleotide) arrays. For example, isolated mRNA from a biologicalsample can be amplified using RT-PCR with random hexamer oroligo(dT)-primer mediated first strand synthesis. The RT-PCR step can beused to detectably-label the amplicons, or, optionally, the ampliconscan be detectably labeled subsequent to the RT-PCR step. For example,the detectable label can be enzymatically (e.g., by nick translation ora kinase such as T4 polynucleotide kinase) or chemically conjugated tothe amplicons using any of a variety of suitable techniques (see, e.g.,Sambrook et al., supra). The detectably-labeled amplicons are thencontacted to a plurality of polynucleotide probe sets, each setcontaining one or more of a polynucleotide (e.g., an oligonucleotide)probe specific for (and capable of binding to) a corresponding amplicon,and where the plurality contains many probe sets each corresponding to adifferent amplicon. Generally, the probe sets are bound to a solidsupport and the position of each probe set is predetermined on the solidsupport. The binding of a detectably-labeled amplicon to a correspondingprobe of a probe set indicates the presence or amount of a target mRNAin the biological sample. Additional methods for detecting mRNAexpression using nucleic acid arrays are described in, e.g., U.S. Pat.Nos. 5,445,934; 6,027,880; 6,057,100; 6,156,501; 6,261,776; and6,576,424; the disclosures of each of which are incorporated herein byreference in their entirety.

Methods of detecting and/or for quantifying a detectable label depend onthe nature of the label. The products of reactions catalyzed byappropriate enzymes (where the detectable label is an enzyme; see above)can be, without limitation, fluorescent, luminescent, or radioactive orthey may absorb visible or ultraviolet light. Examples of detectorssuitable for detecting such detectable labels include, withoutlimitation, x-ray film, radioactivity counters, scintillation counters,spectrophotometers, colorimeters, fluorometers, luminometers, anddensitometers.

RNA can be extracted from the tissue sample by a variety of methods,e.g., the guanidium thiocyanate lysis followed by CsCl centrifugation(Chirgwin et al. 1979, Biochemistry 18:5294-5299). RNA from single cellscan be obtained as described in methods for preparing cDNA librariesfrom single cells, such as those described in Dulac (1998) Curr Top DevBiol 36:245 and Jena et al. (1996) J Immunol Methods 190:199. Care toavoid RNA degradation must be taken, e.g., by inclusion of RNAsin.

The RNA sample can then be enriched in particular species. In oneembodiment, poly(A)+ RNA is isolated from the RNA sample. In general,such purification takes advantage of the poly-A tails on mRNA. Inparticular and as noted above, poly-T oligonucleotides may beimmobilized within on a solid support to serve as affinity ligands formRNA. Kits for this purpose are commercially available, e.g., theMessageMaker kit (Life Technologies, Grand Island, N.Y.).

Types of probes that can be used in the methods described herein includecDNA, riboprobes, synthetic oligonucleotides and genomic probes. Thetype of probe used will generally be dictated by the particularsituation, such as riboprobes for in situ hybridization, and cDNA forNorthern blotting, for example. In one embodiment, the probe is directedto nucleotide regions unique to the RNA. The probes may be as short asis required to differentially recognize marker mRNA transcripts, and maybe as short as, for example, 15 bases; however, probes of at least 17,18, 19 or 20 or more bases can be used. In one embodiment, the primersand probes hybridize specifically under stringent conditions to a DNAfragment having the nucleotide sequence corresponding to the marker. Asherein used, the term “stringent conditions” means hybridization willoccur only if there is at least 95% identity in nucleotide sequences. Inanother embodiment, hybridization under “stringent conditions” occurswhen there is at least 97% identity between the sequences.

The form of labeling of the probes may be any that is appropriate, suchas the use of radioisotopes, for example, ³²P and ³⁵S. Labeling withradioisotopes may be achieved, whether the probe is synthesizedchemically or biologically, by the use of suitably labeled bases.

In certain embodiments, the biological sample contains polypeptidemolecules from the test subject. Alternatively, the biological samplecan contain mRNA molecules from the test subject or genomic DNAmolecules from the test subject.

In other embodiments, the methods further involve obtaining a controlbiological sample from a control subject, contacting the control samplewith a compound or agent capable of detecting marker polypeptide, mRNA,genomic DNA, or fragments thereof, such that the presence of the markerpolypeptide, mRNA, genomic DNA, or fragments thereof, is detected in thebiological sample, and comparing the presence of the marker polypeptide,mRNA, genomic DNA, or fragments thereof, in the control sample with thepresence of the marker polypeptide, mRNA, genomic DNA, or fragmentsthereof in the test sample.

The expression of a fusion protein can also be determined by detectingand/or measuring expression of a protein (e.g., a fusion protein).Methods of determining protein expression generally involve the use ofantibodies specific for the target protein of interest. For example,methods of determining protein expression include, but are not limitedto, western blot or dot blot analysis, immunohistochemistry (e.g.,quantitative immunohistochemistry), immunocytochemistry, enzyme-linkedimmunosorbent assay (ELISA), enzyme-linked immunosorbent spot (ELISPOT;Coligan et al., eds. (1995) Current Protocols in Immunology. Wiley, NewYork), or antibody array analysis (see, e.g., U.S. Patent ApplicationPublication Nos. 20030013208 and 2004171068, the disclosures of each ofwhich are incorporated herein by reference in their entirety). Furtherdescription of many of the methods above and additional methods fordetecting protein expression can be found in, e.g., Sambrook et al.(supra).

In one example, the presence or amount of protein expression can bedetermined using a western blotting technique. For example, a lysate canbe prepared from a biological sample, or the biological sample itself,can be contacted with Laemmli buffer and subjected to sodium-dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE). SDS-PAGE-resolvedproteins, separated by size, can then be transferred to a filtermembrane (e.g., nitrocellulose) and subjected to immunoblottingtechniques using a detectably-labeled antibody specific to the proteinof interest. The presence or amount of bound detectably-labeled antibodyindicates the presence or amount of protein in the biological sample.

In another example, an immunoassay can be used for detecting and/ormeasuring the protein expression of a protein. As above, for thepurposes of detection, an immunoassay can be performed with an antibodythat bears a detection moiety (e.g., a fluorescent agent or enzyme).Proteins from a biological sample can be conjugated directly to asolid-phase matrix (e.g., a multi-well assay plate, nitrocellulose,agarose, sepharose, encoded particles, or magnetic beads) or it can beconjugated to a first member of a specific binding pair (e.g., biotin orstreptavidin) that attaches to a solid-phase matrix upon binding to asecond member of the specific binding pair (e.g., streptavidin orbiotin). Such attachment to a solid-phase matrix allows the proteins tobe purified away from other interfering or irrelevant components of thebiological sample prior to contact with the detection antibody and alsoallows for subsequent washing of unbound antibody. Here as above, thepresence or amount of bound detectably-labeled antibody indicates thepresence or amount of protein in the biological sample.

Methods for generating antibodies or antibody fragments specific for aprotein can be generated by immunization, e.g., using an animal, or byin vitro methods such as phage display. A polypeptide that includes allor part of a target protein can be used to generate an antibody orantibody fragment. The antibody can be a monoclonal antibody or apreparation of polyclonal antibodies.

Methods for detecting or measuring gene expression can optionally beperformed in formats that allow for rapid preparation, processing, andanalysis of multiple samples. This can be, for example, in multi-welledassay plates (e.g., 96 wells or 386 wells) or arrays (e.g., nucleic acidchips or protein chips). Stock solutions for various reagents can beprovided manually or robotically, and subsequent sample preparation(e.g., RT-PCR, labeling, or cell fixation), pipetting, diluting, mixing,distribution, washing, incubating (e.g., hybridization), sample readout,data collection (optical data) and/or analysis (computer aided imageanalysis) can be done robotically using commercially available analysissoftware, robotics, and detection instrumentation capable of detectingthe signal generated from the assay. Examples of such detectors include,but are not limited to, spectrophotometers, luminometers, fluorimeters,and devices that measure radioisotope decay. Exemplary high-throughputcell-based assays (e.g., detecting the presence or level of a targetprotein in a cell) can utilize ArrayScan® VTI HCS Reader or KineticScan®HCS Reader technology (Cellomics Inc., Pittsburgh, Pa.).

As used herein, a subject “at risk for developing” a cancer is a subjecthaving one or more (e.g., two, three, four, five, six, seven, or eightor more) risk factors for developing a cancer. For example, a subject atrisk of developing a cancer may have a predisposition to develop acancer (i.e., a genetic predisposition to develop a cancer such as amutation in a tumor suppressor gene (e.g., mutation in BRCA1, p53, RB,or APC) or has been exposed to conditions that can result in thecondition. Thus, a subject can be one “at risk of developing a cancerwhen the subject has been exposed to mutagenic or carcinogenic levels ofcertain compounds (e.g., carcinogenic compounds in cigarette smoke suchas acrolein, arsenic, benzene, benz[a]anthracene, benzo[a]pyrene,polonium-210 (Radon), urethane, or vinyl chloride). Moreover, thesubject can be “at risk of developing a cancer” when the subject hasbeen exposed to, e.g., large doses of ultraviolet light orX-irradiation, or exposed (e.g., infected) to a tumor-causing/associatedvirus such as papillomavirus, Epstein-Barr virus, hepatitis B virus, orhuman T-cell leukemia-lymphoma virus. Cancer is a class of diseases ordisorders characterized by uncontrolled division of cells and theability of these to spread, either by direct growth into adjacent tissuethrough invasion, or by implantation into distant sites by metastasis(where cancer cells are transported through the bloodstream or lymphaticsystem). Cancer can affect people at all ages, but risk tends toincrease with age. Types of cancers can include, e.g., lung cancer,breast cancer, colon cancer, pancreatic cancer, renal cancer, stomachcancer, liver cancer, bone cancer, hematological cancer, neural tissuecancer (e.g., glioblastoma such as glioblastoma multiforme), melanoma,thyroid cancer, ovarian cancer, testicular cancer, prostate cancer,cervical cancer, vaginal cancer, or bladder cancer.

A subject “suspected of having” a cancer or an infection is one havingone or more symptoms of the cancer or infection. It should be understoodthat mammal at risk for developing, or suspected of having, a cancer oran infection does not include all mammals within the species ofinterest.

In some embodiments, the polypeptides described herein can beadministered as part of a broader therapeutic regimen inclusive of oneor more additional therapies for an indication of interest. That is, apolypeptide described herein may be conjointly administered with otherpharmaceutical agents. Conjoint administration may be accomplished byadministration of a single co-formulation, by simultaneousadministration or by administration at separate times.

In some embodiments, the polypeptides described herein may beparticularly advantageous if administered with other bone-active agents.A patient may benefit from conjointly receiving one or more of thepolypeptides described herein and taking calcium supplements, vitamin D,appropriate exercise and/or, in some cases, other medication. Examplesof other medications include, bisphosphonates (e.g., alendronate,ibandronate and risedronate), calcitonin, estrogens, parathyroid hormoneand raloxifene (see above).

In some embodiments, the polypeptides described herein can beadministered with one or more anti-cancer therapies. Suitableanti-cancer therapies include, e.g., chemotherapeutic agents, ionizingradiation, immunotherapy agents, or hyperthermotherapy. Chemotherapeuticagents include, but are not limited to, aminoglutethimide, amsacrine,anastrozole, asparaginase, bcg, bicalutamide, bleomycin, buserelin,busulfan, camptothecin, capecitabine, carboplatin, carmustine,chlorambucil, cisplatin, cladribine, clodronate, colchicine,cyclophosphamide, cyproterone, cytarabine, dacarbazine, dactinomycin,daunorubicin, dienestrol, diethylstilbestrol, docetaxel, doxorubicin,epirubicin, estradiol, estramustine, etoposide, exemestane, filgrastim,fludarabine, fludrocortisone, fluorouracil, fluoxymesterone, flutamide,gemcitabine, genistein, goserelin, hydroxyurea, idarubicin, ifosfamide,imatinib, interferon, irinotecan, letrozole, leucovorin, leuprolide,levamisole, lomustine, mechlorethamine, medroxyprogesterone, megestrol,melphalan, mercaptopurine, mesna, methotrexate, mitomycin, mitotane,mitoxantrone, nilutamide, nocodazole, octreotide, oxaliplatin,paclitaxel, pamidronate, pentostatin, plicamycin, porfimer,procarbazine, raltitrexed, rituximab, streptozocin, suramin, tamoxifen,taxol, temozolomide, teniposide, testosterone, thioguanine, thiotepa,titanocene dichloride, topotecan, trastuzumab, tretinoin, vinblastine,vincristine, vindesine, and vinorelbine.

These chemotherapeutic anti-tumor compounds may be categorized by theirmechanism of action into groups, including, for example, the following:anti-metabolites/anti-cancer agents, such as pyrimidine analogs(5-fluorouracil, floxuridine, capecitabine, gemcitabine and cytarabine)and purine analogs, folate antagonists and related inhibitors(mercaptopurine, thioguanine, pentostatin and 2-chlorodeoxyadenosine(cladribine)); antiproliferative/antimitotic agents including naturalproducts such as vinca alkaloids (vinblastine, vincristine, andvinorelbine), microtubule disruptors such as taxane (paclitaxel,docetaxel), vincristine, vinblastine, nocodazole, epothilones andnavelbine, epidipodophyllotoxins (etoposide, teniposide), DNA damagingagents (actinomycin, amsacrine, anthracyclines, bleomycin, busulfan,camptothecin, carboplatin, chlorambucil, cisplatin, cyclophosphamide,cytoxan, dactinomycin, daunorubicin, doxorubicin, epirubicin,hexamethylmelamineoxaliplatin, iphosphamide, melphalan, mechlorethamine,mitomycin, mitoxantrone, nitrosourea, plicamycin, procarbazine, taxol,taxotere, teniposide, triethylenethiophosphoramide and etoposide(VP16)); antibiotics such as dactinomycin (actinomycin D), daunorubicin,doxorubicin (adriamycin), idarubicin, anthracyclines, mitoxantrone,bleomycins, plicamycin (mithramycin) and mitomycin; enzymes(L-asparaginase which systemically metabolizes L-asparagine and deprivescells which do not have the capacity to synthesize their ownasparagine); antiplatelet agents; antiproliferative/antimitoticalkylating agents such as nitrogen mustards (mechlorethamine,cyclophosphamide and analogs, melphalan, chlorambucil), ethyleniminesand methylmelamines (hexamethylmelamine and thiotepa), alkylsulfonates-busulfan, nitrosoureas (carmustine (BCNU) and analogs,streptozocin), trazenes-dacarbazinine (DTIC);antiproliferative/antimitotic antimetabolites such as folic acid analogs(methotrexate); platinum coordination complexes (cisplatin,carboplatin), procarbazine, hydroxyurea, mitotane, aminoglutethimide;hormones, hormone analogs (estrogen, tamoxifen, goserelin, bicalutamide,nilutamide) and aromatase inhibitors (letrozole, anastrozole);anticoagulants (heparin, synthetic heparin salts and other inhibitors ofthrombin); fibrinolytic agents (such as tissue plasminogen activator,streptokinase and urokinase), aspirin, dipyridamole, ticlopidine,clopidogrel, abciximab; antimigratory agents; antisecretory agents(breveldin); immunosuppressives (cyclosporine, tacrolimus (FK-506),sirolimus (rapamycin), azathioprine, mycophenolate mofetil);immunomodulatory agents (thalidomide and analogs thereof such aslenalidomide (Revlimid, CC-5013) and CC-4047 (Actimid)),cyclophosphamide; anti-angiogenic compounds (TNP-470, genistein) andgrowth factor inhibitors (vascular endothelial growth factor(VEGF)-inhibitors, fibroblast growth factor (FGF) inhibitors);angiotensin receptor blocker; nitric oxide donors; anti-senseoligonucleotides; antibodies (trastuzumab); cell cycle inhibitors anddifferentiation inducers (tretinoin); mTOR inhibitors, topoisomeraseinhibitors (doxorubicin (adriamycin), amsacrine, camptothecin,daunorubicin, dactinomycin, eniposide, epirubicin, etoposide, idarubicinand mitoxantrone, topotecan, irinotecan), corticosteroids (cortisone,dexamethasone, hydrocortisone, methylprednisolone, prednisone, andprednisolone); growth factor signal transduction kinase inhibitors;mitochondrial dysfunction inducers and caspase activators; and chromatindisruptors.

The term “immunotherapeutic agent” can include any molecule, peptide,antibody or other agent which can stimulate a host immune system togenerate an immune response to a tumor or cancer in the subject. Variousimmunotherapeutic agents are useful in the compositions are known in theart and include, e.g., PD-1 and/or PD-1L inhibitors, CD200 inhibitors,CTLA4 inhibitors, and the like. Exemplary PD-1/PD-L1 inhibitors (e.g.,anti-PD-1 and/or anti-PD-L1 antibodies) are known in the art anddescribed in, e.g., International Patent Application Publication Nos. WO2010036959 and WO 2013/079174, as well as U.S. Pat. Nos. 8,552,154 and7,521,051, the disclosures of each of which as they relate to theantibody descriptions are incorporated herein by reference in theirentirety. Exemplary CD200 inhibitors are also known in the art anddescribed in, e.g., International Patent Application Publication No. WO2007084321. Suitable anti-CTLA4 antagonist agents are described inInternational Patent Application Publication Nos. WO 2001/014424 and WO2004/035607; U.S. Patent Application Publication No. 2005/0201994; andEuropean Patent No. EP 1212422. Additional CTLA-4 antibodies aredescribed in U.S. Pat. Nos. 5,811,097, 5,855,887, 6,051,227, and6,984,720;

In another embodiment, radiation therapy is used. The radiation used inradiation therapy can be ionizing radiation. Radiation therapy can alsobe gamma rays, X-rays, or proton beams. Examples of radiation therapyinclude, but are not limited to, external-beam radiation therapy,interstitial implantation of radioisotopes (I-125, palladium, iridium),radioisotopes such as strontium-89, thoracic radiation therapy,intraperitoneal P-32 radiation therapy, and/or total abdominal andpelvic radiation therapy. For a general overview of radiation therapy,see Hellman, Chapter 16: Principles of Cancer Management: RadiationTherapy, 6th edition, 2001, DeVita et al., eds., J. B. LippencottCompany, Philadelphia. The radiation therapy can be administered asexternal beam radiation or teletherapy wherein the radiation is directedfrom a remote source. The radiation treatment can also be administeredas internal therapy or brachytherapy wherein a radioactive source isplaced inside the body close to cancer cells or a tumor mass. Alsoencompassed is the use of photodynamic therapy comprising theadministration of photosensitizers, such as hematoporphyrin and itsderivatives, Vertoporfin (BPD-MA), phthalocyanine, photosensitizer Pc4,demethoxy-hypocrellin A; and 2BA-2-DMHA.

In some embodiments, hormone therapy is used. Hormonal therapeutictreatments can comprise, for example, hormonal agonists, hormonalantagonists (e.g., flutamide, bicalutamide, tamoxifen, raloxifene,leuprolide acetate (LUPRON), LH-RH antagonists), inhibitors of hormonebiosynthesis and processing, and steroids (e.g., dexamethasone,retinoids, deltoids, betamethasone, cortisol, cortisone, prednisone,dehydrotestosterone, glucocorticoids, mineralocorticoids, estrogen,testosterone, progestins), vitamin A derivatives (e.g., all-transretinoic acid (ATRA)); vitamin D3 analogs; antigestagens (e.g.,mifepristone, onapristone), or antiandrogens (e.g., cyproteroneacetate).

In some embodiments, hyperthermia, a procedure in which body tissue isexposed to high temperatures (up to 106° F.) is used to treat the canceror is selected as a therapy for the subject. Heat may help shrink tumorsby damaging cells or depriving them of substances they need to live.Hyperthermia therapy can be local, regional, and whole-bodyhyperthermia, using external and internal heating devices. Hyperthermiais almost always used with other forms of therapy (e.g., radiationtherapy, chemotherapy, and biological therapy) to try to increase theireffectiveness. Local hyperthermia refers to heat that is applied to avery small area, such as a tumor. The area may be heated externally withhigh-frequency waves aimed at a tumor from a device outside the body. Toachieve internal heating, one of several types of sterile probes may beused, including thin, heated wires or hollow tubes filled with warmwater; implanted microwave antennae; and radiofrequency electrodes. Inregional hyperthermia, an organ or a limb is heated. Magnets and devicesthat produce high energy are placed over the region to be heated. Inanother approach, called perfusion, some of the patient's blood isremoved, heated, and then pumped (perfused) into the region that is tobe heated internally. Whole-body heating is used to treat metastaticcancer that has spread throughout the body. It can be accomplished usingwarm-water blankets, hot wax, inductive coils (like those in electricblankets), or thermal chambers (similar to large incubators).Hyperthermia does not cause any marked increase in radiation sideeffects or complications. Heat applied directly to the skin, however,can cause discomfort or even significant local pain in about half thepatients treated. It can also cause blisters, which generally healrapidly.

In some embodiments, photodynamic therapy (also called PDT,photoradiation therapy, phototherapy, or photochemotherapy) is used forthe treatment of some types of cancer. It is based on the discovery thatcertain chemicals known as photosensitizing agents can kill one-celledorganisms when the organisms are exposed to a particular type of light.PDT destroys cancer cells through the use of a fixed-frequency laserlight in combination with a photosensitizing agent. In PDT, thephotosensitizing agent is injected into the bloodstream and absorbed bycells all over the body. The agent remains in cancer cells for a longertime than it does in normal cells. When the treated cancer cells areexposed to laser light, the photosensitizing agent absorbs the light andproduces an active form of oxygen that destroys the treated cancercells. Light exposure must be timed carefully so that it occurs whenmost of the photosensitizing agent has left healthy cells but is stillpresent in the cancer cells. The laser light used in PDT can be directedthrough a fiber-optic (a very thin glass strand). The fiber-optic isplaced close to the cancer to deliver the proper amount of light. Thefiber-optic can be directed through a bronchoscope into the lungs forthe treatment of lung cancer or through an endoscope into the esophagusfor the treatment of esophageal cancer. An advantage of PDT is that itcauses minimal damage to healthy tissue. However, because the laserlight currently in use cannot pass through more than about threecentimeters of tissue (a little more than one and an eighth inch), PDTis mainly used to treat tumors on or just under the skin or on thelining of internal organs. Photodynamic therapy makes the skin and eyessensitive to light for 6 weeks or more after treatment. Patients areadvised to avoid direct sunlight and bright indoor light for at least 6weeks. If patients must go outdoors, they need to wear protectiveclothing, including sunglasses. Other temporary side effects of PDT arerelated to the treatment of specific areas and can include coughing,trouble swallowing, abdominal pain, and painful breathing or shortnessof breath. In December 1995, the U.S. Food and Drug Administration (FDA)approved a photosensitizing agent called porfimer sodium, or Photofrin®,to relieve symptoms of esophageal cancer that is causing an obstructionand for esophageal cancer that cannot be satisfactorily treated withlasers alone. In January 1998, the FDA approved porfimer sodium for thetreatment of early nonsmall cell lung cancer in patients for whom theusual treatments for lung cancer are not appropriate. The NationalCancer Institute and other institutions are supporting clinical trials(research studies) to evaluate the use of photodynamic therapy forseveral types of cancer, including cancers of the bladder, brain,larynx, and oral cavity.

In some embodiments, laser therapy is used to harness high-intensitylight to destroy cancer cells. This technique is often used to relievesymptoms of cancer such as bleeding or obstruction, especially when thecancer cannot be cured by other treatments. It may also be used to treatcancer by shrinking or destroying tumors. The term “laser” stands forlight amplification by stimulated emission of radiation. Ordinary light,such as that from a light bulb, has many wavelengths and spreads in alldirections. Laser light, on the other hand, has a specific wavelengthand is focused in a narrow beam. This type of high-intensity lightcontains a lot of energy. Lasers are very powerful and may be used tocut through steel or to shape diamonds. Lasers also can be used for veryprecise surgical work, such as repairing a damaged retina in the eye orcutting through tissue (in place of a scalpel). Although there areseveral different kinds of lasers, only three kinds have gained wide usein medicine: Carbon dioxide (CO2) laser: This type of laser can removethin layers from the skin's surface without penetrating the deeperlayers. This technique is particularly useful in treating tumors thathave not spread deep into the skin and certain precancerous conditions.As an alternative to traditional scalpel surgery, the CO2 laser is alsoable to cut the skin. The laser is used in this way to remove skincancers. Neodymium:yttrium-aluminum-garnet (Nd:YAG) laser: light fromthis laser can penetrate deeper into tissue than light from the othertypes of lasers, and it can cause blood to clot quickly. It can becarried through optical fibers to less accessible parts of the body.This type of laser is sometimes used to treat throat cancers. Argonlaser: this laser can pass through only superficial layers of tissue andis therefore useful in dermatology and in eye surgery. It also is usedwith light-sensitive dyes to treat tumors in a procedure known asphotodynamic therapy (PDT). Lasers have several advantages over standardsurgical tools, including: Lasers are more precise than scalpels. Tissuenear an incision is protected, since there is little contact withsurrounding skin or other tissue. The heat produced by lasers sterilizesthe surgery site, thus reducing the risk of infection. Less operatingtime may be needed because the precision of the laser allows for asmaller incision. Healing time is often shortened; since laser heatseals blood vessels, there is less bleeding, swelling, or scarring.Laser surgery may be less complicated. For example, with fiber optics,laser light can be directed to parts of the body without making a largeincision. More procedures may be done on an outpatient basis. Lasers canbe used in two ways to treat cancer: by shrinking or destroying a tumorwith heat, or by activating a chemical—known as a photosensitizingagent—that destroys cancer cells. In PDT, a photosensitizing agent isretained in cancer cells and can be stimulated by light to cause areaction that kills cancer cells. CO2 and Nd:YAG lasers are used toshrink or destroy tumors. They may be used with endoscopes, tubes thatallow physicians to see into certain areas of the body, such as thebladder. The light from some lasers can be transmitted through aflexible endoscope fitted with fiber optics. This allows physicians tosee and work in parts of the body that could not otherwise be reachedexcept by surgery and therefore allows very precise aiming of the laserbeam. Lasers also may be used with low-power microscopes, giving thedoctor a clear view of the site being treated. Used with otherinstruments, laser systems can produce a cutting area as small as 200microns in diameter—less than the width of a very fine thread. Lasersare used to treat many types of cancer. Laser surgery is a standardtreatment for certain stages of glottis (vocal cord), cervical, skin,lung, vaginal, vulvar, and penile cancers. In addition to its use todestroy the cancer, laser surgery is also used to help relieve symptomscaused by cancer (palliative care). For example, lasers may be used toshrink or destroy a tumor that is blocking a patient's trachea(windpipe), making it easier to breathe. It is also sometimes used forpalliation in colorectal and anal cancer. Laser-induced interstitialthermotherapy (LITT) is one of the most recent developments in lasertherapy. LITT uses the same idea as a cancer treatment calledhyperthermia; that heat may help shrink tumors by damaging cells ordepriving them of substances they need to live. In this treatment,lasers are directed to interstitial areas (areas between organs) in thebody. The laser light then raises the temperature of the tumor, whichdamages or destroys cancer cells.

The following examples are intended to illustrate, not to limit, thisdisclosure.

EXAMPLES Example 1. Materials and Methods

TGF-β Family Ligands.

Recombinant Activin A, Activin B, Nodal (3218-ND-025/CF), GDF-1(6937-GD-010/CF), GDF-3 (958-G3-010), GDF-8, GDF-11 (1958-GD-010/CF),TGF-ß-1, BMP-2 (355-BM-010/CF), BMP-4 (314-BP-010/CF), and BMP-9(3209-BP-010/CF) were obtained from R&D Biosystem. Nodal, GDF-3 andGDF-11 are produced in E. coli whereas all other ligands, were expressedusing mammalian cells. (In some instances, different lots of materialproduced in E. coli had different activity.)

Expression Plasmids.

Synthetic human ACTRIIA-hIgG-Fc, ACTRIIB-hIgG-Fc, ALK4-hIgg-Fc, andCryptic-hIgG-Fc genes were obtained from Life Technologies (GeneArt®).Fusion constructs included extracellular domains (ECD) of human ACTRIIA(amino acids 1-120), ACTRIIB (amino acids 1-120), ALK4 (amino acids1-110), and Cryptic (amino acids 1-155). Functional domains were linkedto human IgG1 Fc (SEQ ID NO: 21) via a 22 amino acid long linker (SEQ IDNO:18) containing a TEV cleavage site, a glycine/serine rich region, anda FLAG-tag. Cripto-1 and BMPRII were cloned from cDNA obtained fromThermo Scientific. An amplicon encompassing Criptol (1-161) and BMPRII(1-120) was fused to hIgG1-Fc domain using PCR.

Protein Purification.

ACTRIIA-Fc, ACTRIIB-Fc, ALK4-Fc, BMPRII-Fc, Cryptic-Fc, and Cripto-1-Fc,as well as Activin A, Activin B, GDF-8, TGF-ß-1 were purified fromcondition medium (CHO cell culture) using Protein A capture. Proteinswere eluted with 100 mM Glycine pH 3.0 and immediately neutralized with2 M Tris, pH 9.0. Immobilized Metal Affinity Chromatography was used tocapture Nodal from conditioned medium. Proteins were further purified oranalyzed by size exclusion chromatography to ascertain monodispersity.Purified proteins were dialyzed into phosphate-buffered saline, pH 7.5and stored at −20° C. or −80° C. The purity of the proteins was checkedwith SDS-PAGE or Western Blot under reducing and non-reducingconditions. For inhibition assays, the Fc portion from Fc fusionproteins was removed using Tobacco Etch Virus (TEV) protease followed byProtein A affinity and size exclusion chromatography.

Cell Lines.

A204 cells (HTB-82) and HOS cells (CRL-1543) were obtained from ATCC.Cells were maintained according to ATCC (American Type CultureCollection) culture conditions (RPMI medium supplemented with 10% FBS,0.2 units/ml bovine insulin (SigmaAldrich, 11070-73-8) and 1%penicillin/streptomycin (P/S) mixture). For osteoblast studies, HOScells were maintained in alpha-MEM with 10% FBS and 1% P/S. Cells weregrown at 37° C. under humidified, 5% CO₂ atmosphere. Freshly thawedcells were passaged at least three times before performing assays.

Immunoblotting.

2.0×10⁵ cells were plated in 24-well plates and grown to 80% confluencein complete medium, washed with 1×PBS, starved overnight and grown foradditional 24 hour in serum free medium with or without 39 nM Activin Aor Activin B. Cells were treated with 17.8 or 178 nM Cryptic-1-Fc orACTRIIA-Fc. Protein lysate was prepared by using ice-cold RIPA lysisbuffer (150 mM NaCl, 1% NP40, 0.1% sodium dodecyl sulfate (SDS), 0.5%sodium deoxycholate, 50 mM Tris pH 8.0, 1×‘Recom ProteaseArrest’protease inhibitor cocktail (G-Biosciences, 786-436) and2×PhosphataseArrest′ phosphastase inhibitor cocktail (G-Biosciences,786-450)). Cell lysates were stored at −80° C. Protein concentration oflysates was determined using Bradford. For Western blotting, equalamounts of protein were separated on ‘AnykD’ SDS-polyacrylamide gels(Bio-Rad, 456-9035) under reducing conditions and transferred toHybond-P membranes (GE Healthcare, RPN2020F). Membranes were blockedwith 5% BSA and incubated with primary anti-phospho-Smad2 (CellSignaling, 3108S), anti-Smad2 (Cell Signaling, 5339S) or anti-Actin(Cell Signaling, 3108S) antibodies at 1:1000 dilution, followed byincubation with Horseradish peroxidase conjugated secondary antibody at1:2000 dilution. WesternBright ECL HRP substrate was used for detection(Advansta, K-12043-D20). Western blots were visualized by exposing thegel to autoradiography film (Denville, E3018). Immunoblots werequantified using ImageJ software.

Surface Plasmon Resonance.

Receptor-ligand binding affinities were determined by SPR using theBiacore 2000. Anti-human IgG (Fc) antibody was immobilized onto fourchannels of a CM5 chip using amine coupling chemistry. PurifiedCripto-1-Fc, Cryptic-Fc, ACTRIIA-Fc, ACTRIIB-Fc, BMPRII-Fc or ALK4-Fcwere captured on the experimental flow channels. A reference channel wasmonitored to account for nonspecific binding, drift, and bulk shifts.For kinetic analysis of ligand binding, a concentration series ofligands (Nodal, Activin A, Activin B, GDF-1, GDF-3, GDF-8, GDF-11,TGF-ß-1, BMP-4, BMP-2 and BMP-9) was injected over experimental andcontrol flow channels at 50 μl/min flow rate. For analysis of Cripto-1or Cryptic binding to receptors, Fc-free Cripto-1 or Cryptic at aconcentration of 5 μM was injected over experimental and control flowchannels at 50 μl/min flow rate. For kinetic analysis of ligand bindingin the presence of Cripto-1 or Cryptic, a concentration series ofligands (Nodal, Activin A) combined with excess Cripto-1 or Cryptic (200nM) was injected over experimental and control flow channels at 50μl/min flow rate. For inhibition analysis 1 nM Nodal, Activin A orActivin B was combined with 0 nM, 0.5, 5, 10, 40, 50, 100 or 400 nMFc-free Cripto-1 or Cryptic. The pre-assembled ligand-Cryptic complexeswere injected over experimental and control flow channels at 50 μl/minflow rate. After each binding cycle, the antibody surface wasregenerated to base line. All experiments were carried out at 25° C.HBS-EPS buffer (0.01 M HEPES, 0.5 M NaCl, 3 mM EDTA, 0.005% (v/v) Tween20, pH 7.4) containing 0.1% BSA was used as running buffer. E. coliNodal containing samples were kept without BSA, as the presence of BSAcauses rapid inactivation of recombinant Nodal. Sensograms were analyzedby double referencing. To obtain kinetic rate constants, the processeddata was fitted to 1:1 Langmuir interaction model with mass transportlimitation using Scrubber, Clamp or BiaEvaluation software. Theequilibrium binding constant K_(d) was determined by calculating theratio of binding rate constants k_(d)/k_(a). Results are summarized inTable 1 (below).

Reporter Assays.

About 50,000 A204 cells (ATCC) in complete medium (McCoy's 5A medium(Invitrogen) supplemented with 10% fetal calf serum) were seeded in eachwell of a 96-well plate and grown overnight. The next day, a solutioncontaining 200 ng pNL[NlucP/SBE/Hygro] Vector (experimental luciferasereporter plasmid, firefly luciferase, Promega), 2 ngpNL[NLucP/minP/Hygro] Vector (control luciferase reporter plasmid,renilla luciferase, Promega), 24 μl lipofectamine 2000 (LifeTechnologies), and 960 μl McCoy's 5A medium (Life Technologies) wasprepared and incubated at room temperature for 30 minutes. Afterincubation, 3840 μl McCoy's 5A medium was added to the transfectionsolution, cells were washed with 1×PBS, and 50 μl transfection solutionwas added to each well. Transfection reagent containing medium wasremoved the following day, cells were washed with 1×PBS, and medium wasreplaced with serum free McCoy's 5A medium containing test proteins.After 16 h incubation at 37° C., luciferase activity was detected withthe Dual-Glo Luciferase Assay System (Promega). Chemiluminescence wasmeasured using an Infinite M200 plate reader. Relative luciferase unitswere calculated by dividing firefly luciferase units (FLU) with renillaluciferase units (RLU).

Osteoblast Mineralization Analyses.

HOS cells were plated at 100,000 cells per well of a 12 well plate. Uponreaching confluency, medium was supplemented with 2 mM phosphate and 25μg/ml ascorbic acid. Cells were treated with each feeding (every 2-3days) for 2 weeks with vehicle, 20 μg/ml Cryptic or 50 ng/ml Activin Aalone or together. Cells were rinsed with PBS and fixed in 10% formalinfor 30 minutes at room temperature. Cells were incubated for 1 hour withfreshly made 20 mM alizarin red staining solution, rinsed and digitallyphotographed. Stain was removed with 10% cetylpyridinum chloride andquantitated at 570 nm wavelength.

Statistics.

Cell-based assays were performed in quadruplicates and were repeated atleast two different times. Statistical significance was determined usinga two-tailed T-test. P values <than 0.05 were considered statisticallysignificant.

Example 2. Cryptic and Cripto-1 Expression and Purification

Cryptic and Cripto-1 are secreted proteins that are attached to themembrane via a Glycosylphosphatidylinositol (GPI) anchor (FIG. 1, panelA). A soluble form of human Cryptic and Cripto-1 were expressed inChinese Hamster Ovary (CHO) cells stably transfected with a nucleic acidencoding the soluble forms. The soluble forms included the extracellulardomain of the protein and the Fc portion from human IgG1, linked to eachother via a 22-amino acid linker containing a Tobacco Etch Mosaic Virus(TEV) cleave site (FIG. 1, panel B). For Cryptic, a construct wascreated that included the N-terminal signal peptide and ended at alanine167. For Cripto-1, the signal peptide of Cryptic was used and ended theconstruct at threonine 163, analogous to Cryptic residue alanine 167(FIG. 1, panel A). Cryptic-Fc and Cripto-1-Fc proteins were purifiedfrom conditioned medium by Protein A affinity chromatography, followedby size exclusion chromatography. Approximately 100 mg of purifiedCryptic-Fc and 30 mg of Cripto-1-Fc per liter was obtained of culturecells. Preparative size-exclusion chromatography (SEC) showed thatCryptic could be obtained in an aggregate free form (FIG. 1, panel C).Coomassie-stained SDS-PAGE gels of the purified proteins showed bands ofapproximately 50 kDa under reducing and approximately 100 kDa undernon-reducing conditions, as expected (FIG. 1, panel C).

Example 3. Cryptic and Cripto-1 Bind Distinct Ligands

Surface Plasmon Resonance (SPR) was used to characterize theligand-binding specificities of human Cryptic and Cripto-1. The purifiedFc fusion proteins were captured on a CM5 sensor chip cross-linked withan anti-hFc antibody and subsequently injected different TGFβ familyligands over the captured Cryptic and Cripto-1 at variousconcentrations, including concentrations that far exceeded serum levels(45-47) (FIG. 2, Table 1). Cryptic was shown to bind Activin A andActivin B with very high affinities (k_(a)=3.1×10⁵ (M⁻¹s⁻¹),k_(d)=4.6×10⁻⁵ (s⁻¹), K_(d)=0.15 nM and k_(a)=3.1×10⁵ (M⁻¹s⁻¹),k_(d)=4.6×10⁻⁵ (s⁻¹), K_(d)=0.15 nM), respectively) (FIG. 2, panels Aand B). In addition, Cryptic also bound GDF-8 and GDF-11, albeit withmuch lower affinity than Activin A and Activin B (FIG. 2, panels C andD). Nevertheless, the interaction between Cryptic and GDF-8 or GDF-11 isrelatively stable, as indicated by slow dissociation rates(k_(d)=4.6×10⁻⁴ and 4.6×10⁻⁴ (s⁻¹), respectively. Cryptic also boundNodal; however, the Cryptic-Nodal interaction was several orders ofmagnitude weaker than the Nodal-Cripto-1 interaction (FIG. 2, panel Eand F). Cryptic did not bind appreciably to any other tested TGF-ßfamily ligand, such as TGF-ß-1, GDF-1, GDF-3, BMP-2, BMP-4 and BMP-9(FIG. 2, panel E). These findings indicate that Activin A and Activin Bare the principal ligands that are regulated by Cryptic in humans, andthat Cryptic could also play a role in the regulation of GDF-8 andGDF-11 signaling.

A similar experiment was performed with human Cripto-1, which revealedthat its ligand binding specificity is clearly distinct from that ofCryptic. Of all tested ligands only Nodal bound to human Cripto-1 withappreciable affinity (FIG. 2, panel F). Activin B also bound Cripto-1,however this interaction is unstable as reflected by its fastdissociation rates (k_(d)=4.6×10⁻⁵ (s⁻¹)). Binding of Cripto-1 to anyother tested TGF-ß family ligand, including Activin A, was not observed.These findings therefore indicate that Cripto-1 is very specific forNodal.

Example 4. Cryptic does not Regulate Ligand Binding to ALK4

To establish the role of Cryptic in the ligand-ALK4 interaction, humanALK4-Fc was captured on a sensor chip. To determine whether Crypticbinds ALK4, Fc-free Cryptic was injected at various concentrations. Inthe absence of ligand and other factors, no binding of Cryptic to ALK4was detected, even at concentrations that far exceeded physiologicallevels (e.g. 20 μM) (FIG. 3, panel A). These findings demonstrate thatCryptic does not interact with ALK4 in the absence of other factors.

To determine whether Cryptic enhances or facilitates ligand binding totype I receptors, the effect of Cryptic on the interaction betweenActivin A and ALK4 was studied (FIG. 3, panels B, C and D). HumanALK4-Fc was captured on a sensor chip and contacted with a constantamount of Activin A (1 nM) titrated with Cryptic (0-40 nM) (FIG. 3,panel B) or titrated Activin A (0-40 nM) in the presence of excessCryptic (400 nM) (FIG. 3, panel D). Human Cryptic did not alter theinteraction between Activin A and ALK4. Indeed, the kinetic model forfree Activin A binding to ALK4 is virtually indistinguishable from thatof Activin A binding to ALK4 in the presence of excess human Cryptic(k_(a)=3.1×10⁵ (M⁻¹s⁻¹), k_(d)=4.6×10⁻⁵ (s⁻¹), K_(d)=0.15 nM) (Table 1).Taken together, these findings demonstrate that Cryptic does not play arole in Activin A binding to ALK4.

TABLE 1 Equilibrium binding and rate constants Ligand Analyte k_(a)(M⁻¹s⁻¹) k_(d) (s⁻¹) K_(d) (nM) Cryptic-Fc Activin A 2.0 × 10⁴ 2.0 ×10⁻³ 0.001 Activin B 9.5 × 10⁴ 4.7 × 10⁻⁵ 0.5 GDF-8 5.8 × 10⁴ 1.77 ×10⁻⁴  3.0 GDF-11* 2.9 × 10⁴ 1.1 × 10⁻⁴ 3.8 BMPRII Activin B 5.1 × 10⁵4.2 × 10⁻⁴ 0.8 ALK4 Activin A 4.5 × 10⁵ 1.8 × 10⁻³ 4.0 Activin A +Cryptic 6.2 × 10⁵ 1.6 × 10⁻³ 2.6 *GDF-11 produced by refolding from E.coli (RnD Systems) shows batch variability.

Example 5. Cryptic Inhibits Ligand Binding to Type II Receptors

Next, the effect of Cryptic on ligand binding to the type II receptorswas studied (FIG. 4). Ligands Activin A, Activin B, and GDF-8 wereselected for these studies (FIG. 2). To determine whether Crypticinteracts with type II receptors, human ACTRIIA, ACTRIIB or BMPRII wascaptured on a sensor chip, followed by passing Cryptic over the capturedreceptors. In the absence of ligand, Cryptic did not bind ACTRIIA,ACTRIIB or BMPRII at concentrations that far exceeded physiologicallevels (e.g. 20 μM) (FIG. 3, panel A).

To determine whether Cryptic has an effect on ligand binding to ACTRIIA,ACTRIIB or BMPRII, these receptors were captured on a sensor chip, andActivin A (1 nM), Activin B (10 nM) or GDF-8 (40 nM), preincubated withCryptic at concentrations between 0 and 1600 nM, were passed over thesensor chip. Cryptic inhibited ligand binding to high affinity receptorsin a concentration-dependent manner. The inhibition was observed in thereversed geometry, i.e., with Cryptic-Fc captured on the sensor chip andActivin A, in the presence of varying amounts of ACTRIIA, passed overthe sensor chip (FIG. 4, panel H). Cryptic was further found tocompetitively inhibit the ligand-type II receptor interaction. Thesefindings support the conclusion that human Cryptic binds Activin A,Activin B, and GDF-8 at same site that is bound by the type II receptorsACTRIIA, ACTRIIB and BMPRII.

Example 6. Cryptic Inhibits Activin Signaling

As noted above, the data provided herein show that Cryptic competitivelyinhibits the ligand-type II receptor interaction. While the disclosureis not limited by any particular theory or mechanism of action, Crypticmight also inhibit ligand mediated signal transduction and geneexpression. To examine the potential effect of Cryptic onligand-dependent gene expression, A-204 rhabdomyosarcoma cells weretransfected with pSBE4-luc, a Smad-2/3-responsive reporter, andpRL-CMV-luc as control (Zawal et al. (1998) Mol Cell 1:611-617). Thetransfected cells were treated with 10 nM Activin A or Activin B anddifferent concentrations of Cryptic-Fc (FIG. 5, panel A and C). Bothligands strongly induced Luciferase reporter activity (approximately 8fold relative to control) and that Cryptic-Fc inhibited the liganddependent luciferase signal in a concentration dependent manner (FIG. 5,panels A and C). Indeed, Cryptic-Fc inhibited Activin A and Activin Binduced Luciferase reporter activity with as well as the bone fideActivin inhibitor ACTRIIA-Fc (FIG. 5, panel B and D). For signaltransduction, a phospho-Smad2 Western blot was performed (FIG. 5, panelB and D). A-204 cells were also treated with 10 nM ligand and titratedCryptic-Fc. Activin A and Activin B induced and Cryptic-Fc inhibitedSmad-2 phosphorylation. Indeed, Cryptic-Fc inhibited Smad-2phosphorylation with similar potency as ACTRIIA-Fc (FIG. 5, panel B andD).

Given that Activin A inhibits and Activin A inhibitors promoteosteoblast mineralization (see, e.g., Pear, Cryptic-Fc has an effect onosteoblast mineralization in the presence of Activin A. Human HOS cellswere grown to confluence and induced to differentiate (by addition ofphosphate and vitamin C) in the presence or absence of Activin A (50ng/ml) with or without Cryptic. As expected, addition of Activin Aprevents osteoblast mineralization (FIG. 5, panel E and F). Strikingly,10 μg/ml Cryptic-Fc prevented the Activin A suppression ofmineralization (FIG. 5, panel E and F). In summary, our results fromthree different in vitro experiments demonstrate that Cryptic-Fcefficiently inhibits Activin A mediated signaling with physiologicallyrelevant outcomes, including the restoration of osteoblastmineralization (FIG. 5).

While the present disclosure has been described with reference to thespecific embodiments thereof, it should be understood by those skilledin the art that various changes may be made and equivalents may besubstituted without departing from the true spirit and scope of thedisclosure. In addition, many modifications may be made to adapt aparticular situation, material, composition of matter, process, processstep or steps, to the objective, spirit and scope of the presentdisclosure. All such modifications are intended to be within the scopeof the disclosure.

1. A polypeptide comprising: (i) the amino acid sequence depicted in anyone of SEQ ID NOs:1 to 9, 19, or 20; (ii) a variant of the amino acidsequence depicted in any one of SEQ ID NOs: 1 to 9, 19, or 20 having notmore than 10 amino acid substitutions, deletions, or insertions; or(iii) an amino acid sequence that is at least 80% identical to any oneof the amino acid sequences depicted in SEQ ID NOs: 1 to 9, 19, or 20.2. The polypeptide of claim 1, wherein the polypeptide comprises theamino acid sequence depicted in SEQ ID NO:7-9, 19, or
 20. 3. Thepolypeptide of claim 1, wherein the polypeptide comprises an amino acidsequence comprising any one of SEQ ID NOs: 4 to 9, and wherein the aminoacid sequence of the polypeptide is at least 80% identical to SEQ ID NO:1 or
 2. 4. The polypeptide of claim 1, wherein the polypeptide binds tohuman Activin A with a K_(D) selected from the group consisting of lessthan 1×10⁻⁹M, 1×10⁻¹⁰ M, and 1×10⁻¹¹M. 5-6. (canceled)
 7. Thepolypeptide of claim 1, wherein the polypeptide has at least 30% of theability of wild-type human Cryptic to inhibit human Activin A-dependentcell signaling in vitro or B-dependent cell signaling in vitro.
 8. Thepolypeptide claim 1, wherein the polypeptide binds to human Activin Bwith a K_(D) of less than 1×10⁻⁹M or 5×10⁻¹⁰ M. 9-10. (canceled)
 11. Thepolypeptide of claim 1, wherein the polypeptide comprises a heterologousmoiety that increases the serum half-life of the peptide in a subject.12. The polypeptide of claim 11, wherein the heterologous moietycomprises an immunoglobulin Fc constant region having an amino acidsequence selected from the group consisting of SEQ ID NO: 21, SEQ ID NO:10, SEQ ID NO: 19, and SEQ ID NO:
 20. 13-15. (canceled)
 16. Thepolypeptide of claim 11, wherein the heterologous moiety comprises allor a portion of an albumin protein or polyethylene glycol. 17.(canceled)
 18. The polypeptide of claim 1, wherein the polypeptidecomprises a heterologous moiety that targets the polypeptide to bonewherein said moiety comprises the formula: X_(n), wherein X is acanonical or noncanonical amino acid that has a negative charge atphysiological pH and n is an integer from 1 to 25, and wherein saidamino acid is aspartic acid or glutamic acid. 19-20. (canceled)
 21. Thepolypeptide of claim 18, wherein n is an integer between 5 and 15 or 10and
 16. 22. (canceled)
 23. The polypeptide of claim 1, wherein thepolypeptide comprises a detectable label.
 24. A method for increasingbone growth, bone strength, or bone density in a subject in needthereof, the method comprising administering to the subject one or moreof any one of the polypeptides according to claim 1 in an amountsufficient to increase bone growth, bone strength, or bone density inthe subject.
 25. The method of claim 24, wherein the subject has acondition associated with bone loss.
 26. The method of claim 25, whereinthe condition is selected from the group consisting of osteoporosis,Paget's disease, rheumatoid arthritis, periodontal disease, bonefracture, bone deficiency, metastatic bone disease, osteoarthritis,primary or secondary hyperparathyroidism, and osteolytic bone disease.27-28. (canceled)
 29. The method of claim 26, wherein the periodontaldisease is gingivitis or periodontitis.
 30. The method of claim 24,wherein, following administration, the composition improves a boneparameter selected from the group consisting of bone volume density,total bone surface, bone surface density, trabecular number, trabecularthickness, trabecular spacing, and total volume.
 31. The method of claim24, further comprising monitoring the subject for an improvement in anyone of the following bone parameters: bone volume density, total bonesurface, bone surface density, trabecular number, trabecular thickness,trabecular spacing, or total volume.
 32. The method of claim 24, furthercomprising administering to the subject at least one additionaltherapeutic agent that promotes bone growth or inhibits bone resorption.33. A method for increasing muscle mass or muscle strength in a subjectin need thereof, the method comprising administering to the subject oneor more of any of the polypeptides according to claim 1 in an amountsufficient to increase muscle mass or muscle strength in the subject.34. The method of claim 33, wherein the subject has a muscle wastingdisorder.
 35. A method for treating a subject having a muscle-wastingdisorder or muscle atrophy, the method comprising administering to thesubject one or more of any of the polypeptides according to claim 1 inan amount sufficient to treat the muscle-wasting disorder or muscleatrophy.
 36. The method of claim 34 or 35, wherein the muscle-wastingcondition is, or is associated with, Duchenne muscular dystrophy (DMD),multiple types of limb girdle MD (LGMD), other congenital MDs (CMD),sarcopenia, cancer cachexia, or Diabetes mellitus.
 37. A method fortreating a musculoskeletal disorder in a subject, the method comprisingadministering to the subject one or more of any of the polypeptidesaccording to claim 1 in an amount sufficient to treat themusculoskeletal disorder.
 38. The method of claim 37, wherein themusculoskeletal disorder is: (i) osteoporosis, (ii) osteopenia, (iii)sarcopenia, (iv) arthritis, (v) tissue atrophy, (vi) periodontaldisease, (vii) wound healing, or (viii) bone loss due to malignancy,endocrine disorders, arthritis, immobility, or disuse.
 39. A method fortreating a subject having a metabolic disorder, the method comprisingadministering to the subject one or more of any of the polypeptidesaccording to claim 1 in an amount sufficient to treat the metabolicdisorder.
 40. The method of claim 39, wherein the metabolic disorder istype 2 diabetes, noninsulin-dependent diabetes mellitus, hyperglycemia,and obesity.
 41. A method for treating a subject having a cancer, themethod comprising administering to the subject one or more of any of thepolypeptides according to claim 1 in an amount sufficient to treat thecancer.
 42. The method of claim 41, wherein the cancer comprises cancercells that express one or more receptors for Activin A or Activin B. 43.The method of claim 42, wherein one or both of the proliferation andviability of the cancer cells is positively regulated by Activin A orActivin B.
 44. The method of claim 41, wherein the cancer is a lungcancer, breast cancer, colon cancer, pancreatic cancer, renal cancer,stomach cancer, liver cancer, bone cancer, hematological cancer, neuraltissue cancer, melanoma, thyroid cancer, ovarian cancer, testicularcancer, prostate cancer, cervical cancer, vaginal cancer, or bladdercancer.
 45. The method of any one of claim 24, 33, 35, 37, 39, or 41,wherein the polypeptide is administered to the subject intravenously orsubcutaneously.
 46. (canceled)
 47. The method of any one of claim 24,33, 35, 37, 39, or 41, wherein the subject is a human.
 48. A fusionpolypeptide, comprising: an N-terminal region comprising a signalpeptide sequence from a cryptic protein or a functional variant orfragment thereof; and a fragment of a human Cripto-1 protein comprising:an EGF domain; and a CFC domain.